Synthetic peptides and uses therefore

ABSTRACT

Aspects of the present invention are related to a synthetic polypeptide comprising a plurality of different segments from one or more parent polypeptides, linked together in such a way that is different from their linkage in the one or more parent polypeptides, in such way as to impede, abrogate or otherwise alter at least one function associated with the linkage in the one or more parent polypeptides, and in such a way that their product is not similar in function and/or structure to at least a portion of the one or more parent polypeptides. Additional aspects include a synthetic polynucleotide encoding the synthetic polypeptide, methods of production, a synthetic construct and methods of using the synthetic polypeptide, nucleotide construct and compositions comprising the above. Another aspect is directed towards a computer program product for designing these synthetic polypeptides and polynucleotides.

CROSS-REFERENCE TO RELATED APPLICATIONS

This is the U.S. National Phase under 35 U.S.C. §371 of International Application No. PCT/AU01/00622, filed May 25, 2001, designating the United States and published in English, which claims priority to Australian Application No. PQ 7761, filed May 26, 2000, the disclosure of which is herein incorporated by reference in its entirety.

FIELD OF THE INVENTION

THIS INVENTION relates generally to agents for modulating immune responses. More particularly, the present invention relates to a synthetic polypeptide comprising a plurality of different segments of a parent polypeptide, wherein the segments are linked to each other such that one or more functions of the parent polypeptide are impeded, abrogated or otherwise altered and such that the synthetic polypeptide, when introduced into a suitable host, can elicit an immune response against the parent polypeptide. The invention also relates to synthetic polynucleotides encoding the synthetic polypeptides and to synthetic constructs comprising these polynucleotides. The invention further relates to the use of the polypeptides and polynucleotides of the invention in compositions for modulating immune responses. The invention also extends to methods of using such compositions for prophylactic and/or therapeutic purposes.

Bibliographic details of various publications referred to in this specification are collected at the end of the description.

BACKGROUND OF THE INVENTION

The modem reductionist approach to vaccine and therapy development has been pursued for a number of decades and attempts to focus only on those parts of pathogens or of cancer proteins which are relevant to the immune system. To date the performance of this approach has been relatively poor considering the vigorous research carried out and the number of effective vaccines and therapies that it has produced. This approach is still being actively pursued, however, despite its poor performance because vaccines developed using this approach are often extremely safe and because only by completely understanding the immune system can new vaccine strategies be developed.

One area that has benefited greatly from research efforts is knowledge about how the adaptive immune system operates and more specifically how T and B cells learn to recognise specific parts of pathogens and cancers. T cells are mainly involved in cell-mediated immunity whereas B cells are involved in the generation of antibody-mediated immunity. The two most important types of T cells involved in adaptive cellular immunity are αβ CD8⁺ cytotoxic T lymphocytes (CTL) and CD4⁺ T helper lymphocytes. CTL are important mediators of cellular immunity against many viruses, tumours, some bacteria and some parasites because they are able to kill infected cells directly and secrete various factors which can have powerful effects on the spread of infectious organisms. CTLs recognise epitopes derived from foreign intracellular proteins, which are 8-10 amino acids long and which are presented by class I major histocompatibility complex (MHC) molecules (in humans called human lymphocyte antigens—HLAs) (Jardetzky et al., 1991; Fremont et al., 1992; Rotzschke et al., 1990). T helper cells enhance and regulate CTL responses and are necessary for the establishment of long-lived memory CTL. They also inhibit infectious organisms by secreting cytokines such as IFN-γ. T helper cells recognise epitopes derived mostly from extracellular proteins which are 12-25 amino acids long and which are presented by class II MHC molecules (Chicz et al., 1993; Newcomb et al., 1993). B cells, or more specifically the antibodies they secrete, are important mediators in the control and clearance of mostly extracellular organisms. Antibodies recognise mainly conformational determinants on the surface of organisms, for example, although sometimes they may recognise short linear determinants.

Despite significant advances towards understanding how T and linear B cell epitopes are processed and presented to the immune system, the full potential of epitope-based vaccines has not been fully exploited. The main reason for this is the large number of different T cell epitopes, which have to be included into such vaccines to cover the extreme HLA polymorphism in the human population. The human HLA diversity is one of the main reasons why whole pathogen vaccines frequently provide better population coverage than subunit or peptide-based vaccine strategies. There is a range of epitope-based strategies though which have tried to solve this problem, e.g. peptide blends, peptide conjugates and polyepitope vaccines (ie comprising strings of multiple epitopes) (Dyall et al., 1995; Thomson et al., 1996; Thomson et al., 1998; Thomson et al., 1998). These approaches however will always be sub optimal not only because of the slow pace of epitope characterisation but also, because it is virtually impossible for them to cover every existing HLA polymorphism in the population. A number of strategies have sought to avoid both problems by not identifying epitopes and instead incorporating larger amounts of sequence information e.g., approaches using whole genes or proteins and approaches that mix multiple protein or gene sequences together. The proteins used by these strategies however sometimes still function and therefore can compromise vaccine safety e.g. whole cancer proteins. Alternative strategies have tried to improve the safety of vaccines by fragmenting the genes and expressing them either separately or as complex mixtures e.g., library DNA immunisation or by ligating such fragments back together. These approaches are still sub-optimal because they are too complex, generate poor levels of immunity, cannot guarantee that all proteins no longer function and/or that all fragments are present, which compromises substantially complete immunological coverage.

The lack of a safe and efficient vaccine strategy that can provide substantially complete immunological coverage is an important problem, especially when trying to develop vaccines against rapidly mutating and persistent viruses such as HIV and hepatitis C virus, because partial population coverage could allow vaccine-resistant pathogens to re-emerge in the future. Human immunodeficiency virus (HIV) is an RNA lentivirus virus approximately 9 kb in length, which infects CD4⁺ T cells, causing T cell decline and AIDS typically 3-8 years after infection. It is currently the most serious human viral infection, evidenced by the number of people currently infected with HIV or who have died from AIDS, estimated by the World Health Organisation (WHO) and UNAIDS in their AIDS epidemic update (December 1999) to be 33.6 and 16.3 million people, respectively. The spread of HIV is also now increasing fastest in areas of the world where over half of the human population reside, hence an effective vaccine is desperately needed to curb the spread of this epidemic. Despite the urgency, an effective vaccine for HIV is still some way off because of delays in defining the correlates of immune protection, lack of a suitable animal model, existence of up to 8 different subtypes of HIV and a high HIV mutation rate.

A significant amount of research has been carried out to try and develop a vaccine capable of generating neutralising antibody responses that can protect against field isolates of HIV. Despite these efforts, it is now clear that the variability, instability and inaccessibility of critical determinants on the HIV envelope protein will make it extremely difficult and perhaps impossible to develop such a vaccine (Kwong et al., 1998). The limited ability of antibodies to block HIV infection is also supported by the observation that development of AIDS correlates primarily with a reduction in CTL responsiveness to HIV and not to altered antibody levels (Ogg et al., 1998). Hence CTL-mediated and not antibody-mediated responses appear to be critical for maintaining the asymptomatic state in vivo. There is also some evidence to suggest that pre-existing HIV-specific CTL responses can block the establishment of a latent HIV infection. This evidence comes from a number of cases where individuals have generated HIV-specific CTL responses without becoming infected and appear to be protected from establishing latent HIV infections despite repeated virus exposure (Rowland-Jones et al., 1995; Parmiani 1998). Taken together, these observations suggest that a vaccine capable of generating a broad range of strong CTL responses may be able to stop individuals from becoming latently infected with HIV or at least allow infected individuals to remain asymptomatic for life. Virtually all of the candidate HIV vaccines developed to date have been derived from subtype B HIV proteins (western world subtype) whereas the majority of the HIV infections worldwide are caused by subtypes A/E or C (E and A are similar except in the envelop protein)(referred to as developing world subtypes). Hence existing candidate vaccines may not be suitable for the more common HIV subtypes. Recently, there has been some evidence that B subtype vaccines may be partially effective against other common HIV subtypes (Rowland-Jones et al., 1998). Accordingly, the desirability of a vaccine still remains, whose effectiveness is substantially complete against all isolates of all strains of HIV.

SUMMARY OF THE INVENTION

The present invention is predicated in part on a novel strategy for enhancing the efficacy of an immunopotentiating composition. This strategy involves utilising the sequence information of a parent polypeptide to produce a synthetic polypeptide that comprises a plurality of different segments of the parent polypeptide, which are linked sequentially together in a different arrangement relative to that of the parent polypeptide. As a result of this change in relationship, the sequence of the linked segments in the synthetic polypeptide is different to a sequence contained within the parent polypeptide. As more fully described hereinafter, the present strategy is used advantageously to cause significant disruption to the structure and/or function of the parent polypeptide while minimising the destruction of potentially useful epitopes encoded by the parent polypeptide.

Thus, in one aspect of the present invention, there is provided a synthetic polypeptide comprising a plurality of different segments of at least one parent polypeptide, wherein the segments are linked together in a different relationship relative to their linkage in the at least one parent polypeptide.

In one embodiment, the synthetic polypeptide consists essentially of different segments of a single parent polypeptide.

In an alternate embodiment, the synthetic polypeptide consists essentially of different segments of a plurality of different parent polypeptides.

Suitably, said segments in said synthetic polypeptide are linked sequentially in a different order or arrangement relative to that of corresponding segments in said at least one parent polypeptide.

Preferably, at least one of said segments comprises partial sequence identity or homology to one or more other said segments. The sequence identity or homology is preferably contained at one or both ends of said at least one segment.

In another aspect, the invention resides in a synthetic polynucleotide encoding the synthetic polypeptide as broadly described above.

According to yet another aspect, the invention contemplates a synthetic construct comprising a said polynucleotide as broadly described above that is operably linked to a regulatory polynucleotide.

In a further aspect of the invention, there is provided a method for producing a synthetic polynucleotide as broadly described above, comprising:

-   -   linking together in the same reading frame a plurality of         nucleic acid sequences encoding different segments of at least         one parent polypeptide to form a synthetic polynucleotide whose         sequence encodes said segments linked together in a different         relationship relative to their linkage in the at least one         parent polypeptide.

Preferably, the method further comprises fragmenting the sequence of a respective parent polypeptide into fragments and linking said fragments together in a different relationship relative to their linkage in said parent polypeptide sequence. In a preferred embodiment of this type, the fragments are randomly linked together.

Suitably, the method further comprises reverse translating the sequence of a respective parent polypeptide or a segment thereof to provide a nucleic acid sequence encoding said parent polypeptide or said segment. In a preferred embodiment of this type, an amino acid of said parent polypeptide sequence is reverse translated to provide a codon, which has higher translational efficiency than other synonymous codons in a cell of interest. Suitably, an amino acid of said parent polypeptide sequence is reverse translated to provide a codon which, in the context of adjacent or local sequence elements, has a lower propensity of forming an undesirable sequence (e.g., a palindromic sequence or a duplicated sequence) that is refractory to the execution of a task (e.g., cloning or sequencing).

In another aspect, the invention encompasses a computer program product for designing the sequence of a synthetic polypeptide as broadly described above, comprising:

-   -   code that receives as input the sequence of at least one parent         polypeptide;     -   code that fragments the sequence of a respective parent         polypeptide into fragments;     -   code that links together said fragments in a different         relationship relative to their linkage in said parent         polypeptide sequence; and     -   a computer readable medium that stores the codes.

In yet another aspect, the invention provides a computer program product for designing the sequence of a synthetic polynucleotide as broadly described above, comprising:

-   -   code that receives as input the sequence of at least one parent         polypeptide;     -   code that fragments the sequence of a respective parent         polypeptide into fragments;     -   code that reverse translates the sequence of a respective         fragment to provide a nucleic acid sequence encoding said         fragment;     -   code that links together in the same reading frame each said         nucleic acid sequence to provide a polynucleotide sequence that         codes for a polypeptide sequence in which said fragments are         linked together in a different relationship relative to their         linkage in the at least one parent polypeptide sequence; and     -   a computer readable medium that stores the codes.

In still yet another aspect, the invention provides a computer for designing the sequence of a synthetic polypeptide as broadly described above, wherein said computer comprises:

-   -   (a) a machine-readable data storage medium comprising a data         storage material encoded with machine-readable data, wherein         said machine-readable data comprise the sequence of at least one         parent polypeptide;     -   (b) a working memory for storing instructions for processing         said machine-readable data;     -   (c) a central-processing unit coupled to said working memory and         to said machine-readable data storage medium, for processing         said machine readable data to provide said synthetic polypeptide         sequence; and     -   (d) an output hardware coupled to said central processing unit,         for receiving said synthetic polypeptide sequence.

In a preferred embodiment, the processing of said machine readable data comprises fragmenting the sequence of a respective parent polypeptide into fragments and linking together said fragments in a different relationship relative to their linkage in the sequence of said parent polypeptide.

In still yet another aspect, the invention resides in a computer for designing the sequence of a synthetic polynucleotide as broadly described above, wherein said computer comprises:

-   -   (a) a machine-readable data storage medium comprising a data         storage material encoded with machine-readable data, wherein         said machine-readable data comprise the sequence of at least one         parent polypeptide;     -   (b) a working memory for storing instructions for processing         said machine-readable data;     -   (c) a central-processing unit coupled to said working memory and         to said machine-readable data storage medium, for processing         said machine readable data to provide said synthetic         polynucleotide sequence; and     -   (d) an output hardware coupled to said central processing unit,         for receiving said synthetic polynucleotide sequence.

In a preferred embodiment, the processing of said machine readable data comprises fragmenting the sequence of a respective parent polypeptide into fragments, reverse translating the sequence of a respective fragment to provide a nucleic acid sequence encoding said fragment and linking together in the same reading frame each said nucleic acid sequence to provide a polynucleotide sequence that codes for a polypeptide sequence in which said fragments are linked together in a different relationship relative to their linkage in the at least one parent polypeptide sequence.

According to another aspect, the invention contemplates a composition, comprising an immunopotentiating agent selected from the group consisting of a synthetic polypeptide as broadly described above, a synthetic polynucleotide as broadly described above and a synthetic construct as broadly described above, together with a pharmaceutically acceptable carrier.

The composition may optionally comprise an adjuvant.

In a further aspect, the invention encompasses a method for modulating an immune response, which response is preferably directed against a pathogen or a cancer, comprising administering to a patient in need of such treatment an effective amount of an immunopotentiating agent selected from the group consisting of a synthetic polypeptide as broadly described above, a synthetic polynucleotide as broadly described above and a synthetic construct as broadly described above, or a composition as broadly described above.

According to still a further aspect of the invention, there is provided a method for treatment and/or prophylaxis of a disease or condition, comprising administering to a patient in need of such treatment an effective amount of an immunopotentiating agent selected from the group consisting of a synthetic polypeptide as broadly described above, a synthetic polynucleotide as broadly described above and a synthetic construct as broadly described above, or a composition as broadly described above.

The invention also encompasses the use of the synthetic polypeptide, the synthetic polynucleotide and the synthetic construct as broadly described above in the study, and modulation of immune responses.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagrammatic representation showing the number of people living with AIDS in 1998 in various parts of the world and most prevalent HIV clades in these regions. Estimates generated by UNAIDS.

FIG. 2 is a graphical representation showing trends in the incidence of the common HIV clades and estimates for the future. Graph from the International Aids Vaccine Initiative (IAVI).

FIG. 3 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV gag [SEQ ID NO: 1] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV clade consensus sequences for the HIV gag protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR 98-485.

FIG. 4 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV pol [SEQ ID NO: 2] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV lade consensus sequences for the HIV pol protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR98-485.

FIG. 5 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV vif [SEQ ID NO: 3] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV clade consensus sequences for the HIV vif protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR98-485.

FIG. 6 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV vpr [SEQ ID NO: 4] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV lade consensus sequences for the HIV vpr protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR 98-485.

FIG. 7 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV tat [SEQ ID NO: 5] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV lade consensus sequences for the HIV tat protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR 98-485.

FIG. 8 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV rev [SEQ ID NO: 6] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV lade consensus sequences for the HIV rev protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR 98-485.

FIG. 9 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV vpu [SEQ ID NO: 7] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV lade consensus sequences for the HIV vpu protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR 98-485.

FIG. 10 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV env [SEQ ID NO: 8] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV clade consensus sequences for the HIV env protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR 98-485.

FIG. 11 is a diagrammatic representation showing overlapping segments of a parent polypeptide sequence for HIV nef [SEQ ID NO: 9] used for the construction of an embodiment of an HIV Savine. Also shown are the alignments of common HIV clade consensus sequences for the HIV nef protein from the HIV Molecular Immunology Database 1997, Editors Bette Korber, John Moore, Cristian Brander, Richard Koup, Barton Haynes and Bruce Walker. Publisher, Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, N.Mex., Pub LAUR 98-485.

FIG. 12 is a diagrammatic representation depicting the systematic segmentation of the designed degenerate consensus sequences for each HIV protein and the reverse translation of each segment into a DNA sequence. Also shown is the number of segments used during random rearrangement and amino acids that were removed. Amino acids surrounded by an open square were removed from the design, because degenerate codons to cater for the desired amino acid combination required too many degenerate bases to comply with the incorporation of degenerate sequence rules outlined in the description of the invention herein. Amino acids surrounded by an open circle were removed only in the segment concerned mainly because they were coded for in an oligonucleotide overlap region. Amino acids marked with an asterisk were designed differently in one fragment compared to the corresponding overlap region (see tat gene)

FIG. 13 is a diagrammatic representation showing the first and second most frequently used codons in mammals used to reverse translate HIV protein segments. Also shown are all first and second most frequently used degenerate codons for two amino acids where only one base is varied. Codons used where more than one base was varied were worked out in each case by comparing all the codons for each amino acid. The IUPAC codes for degenerate bases are also shown.

FIG. 14 illustrates the construction plan for the HIV Savine showing the approximate sizes of the subcassettes, cassettes and full-length Savine cDNA and the restriction sites involved in joining them together. Also shown are the extra sequences added onto each subcassette during their design and a brief description of how the subcassettes, cassettes and full length cDNA were constructed and transferred into appropriate DNA plasmids. Description of full length construction: pA was cleaved with XhoI/SalI and cloned into XhoI arms of the B cassette; pAB was cleaved with XhoI and cloned into XhoI arms of the C cassette; full length construct is excisable with either XbaI/BamHI at the 5′ end or BglII at the 3′ end. Options for excising cassettes: A) XbaI/BamHI at the 5′ end, BglII/XhoI at the 3′ end; B) XbaI/BamHI at the 5′ end, BglII/SalI at the 3′ end; C) XbaI/BamHI at the 5′ end, BglII/SalI at the 3′ end. Cleaving plasmid vectors: pDNAVacc is cleavable with XbaI/XhoI (DNA vaccination); pBCB07 or pTK7.5 vectors are cleavable with BamHI/SalI (Recombinant Vaccinia); pAvipox vector pAF09 is cleavable with BamHI/SalI (Recombinant Avipox).

FIG. 15 shows the full length DNA (17253 bp) and protein sequence (5742 aas) of the HIV Savine construct. Fragment boundaries are shown, together with the position of each fragment in each designed HIV protein, fragment number (in brackets), spacer residues (two alanine residues) and which fragment the spacer was for (open boxes and arrows). The location of residual restriction site joining sequences corresponding to subcassette or cassette boundaries (shaded boxes) are also shown, along with start and stop codons, Kozak sequence, the location of the murine influenza virus CTL epitope sequence (near the 3′ end), important restriction sites at each end and the position of each degenerate amino acid (indicated by ‘X’).

FIG. 16 depicts the layout and position of oligonucleotides in the designed DNA sequence for subcassette A1. The sequences which anneal to the short amplification oligonucleotides are indicated by hatched boxes and the position of oligonucleotide overlap regions are dark shaded.

FIG. 17: Panel (a) depicts the stepwise asymmetric PCR of the two halves of subcassette A1 (lanes 2-5 and 7-9, respectively) and final splicing together by SOEing (lane 10). DNA standards in lane 1 are pUC18 digested with Sau3AI. Panel (b) shows the stepwise ligation-mediated joining and PCR amplification of each cassette as indicated. DNA standards in lane 1 are SPP1 cut with EcoRI.

FIG. 18: Panel (a) shows summary of the construction of the DNA vaccine plasmids that express one HIV Savine cassette. Panel (b) shows a summary of the construction of the plasmids used for marker rescue recombination to generate Vaccinia viruses expressing one HIV Savine cassette. Panel (c) shows a summary of the construction of the DNA vaccine plasmids which each express a version of the full-length HIV Savine cDNA

FIG. 19 shows restimulation of HIV specific polyclonal CTL responses from three HIV-infected patients by the HIV Savine constructs. PBMCs from three different patients were restimulated for 7 days by infection with Vaccinia virus pools expressing the HIV Savine cassettes: Pool 1 included VV-AC1 and VV-BC1; Pool 2 included VV-AC2, VV-BC2 and VV-CC2. The restimulated PBMCs were then mixed with autologous LCLs (effector to target ratio of 50:1), which were either uninfected or infected with either Vaccinia viruses expressing the HIV proteins gag (VV-gag), env (VV-env) or pol (VV-pol), VV-HIV Savine pools 1 (light bars) or 2 (dark bars) or a control Vaccinia virus (VV-Lac) and the amount of ⁵¹Cr released used to determine percent specific lysis. K562 cells were used to determine the level of NK cell-mediated killing in their stimulated culture.

FIG. 20 is a diagrammatic representation showing CD4+ proliferation of PBMCs from HIV-1 infected patients restimulated with either Pool1 or Pool2 of the HIV-1 Savine. Briefly PBMCs were stained with CFSE and culture for 6 days with or without VVs encoding either pooh or pool2 of the HIV-1 Savine. Restimulated Cells were then labelled with antibodies and analysed by FACS.

FIG. 21 is a graphical representation showing the CTL response in mice vaccinated with the HIV Savine. C57BL6 mice were immunised with the HIV-1 Savine DNA vaccine comprising the six plasmids described in FIG. 18 a (100 μg total DNA was given as 50 μg/leg i.m.). One week later Poxviruses (1×10⁷ pfu) comprising Pool 1 of the HIV-1 Savine were used to boost the immune responses. Three weeks later splenocytes from these mice were restimulated with VV-Pool 1 or VV-Pool 2 for 5 days and the resultant effectors used in a ⁵¹Cr release cytotoxicity assay against targets infected with CTRVV, VV-pools or VV expressing the natural antigens from HIV-1.

FIG. 22 shows immune responses of HIV Immune Macaques (vaccinated with recombinant FPV expressing gag-pol and challenged with HIV-1 2 years prior to experiment). Monkeys 1 and 2 were immunised once at day 0 with VV Savine pool 1 (Three VVs which together express the entire HIV Savine). Monkey 3 was immunised twice with FPV-gag-pol ie., Day 0 is 3 weeks after first FPV-gag-pol immunisation. A) IFN-γ detection by ELISPOT of whole blood (0.5 mL, venous blood heparin-anticoagulated) stimulated with Aldrithiol-2 inactivated whole HIV-1 (20 hours, 20 μg/mL). Plasma samples were then centrifuged (1000×g) and assayed in duplicate for antigen-specific IFN using capture ELISA. B) Flow cytometric detection of HIV-1 specific CD69+/CD8+ T cells. Freshly isolated PBMCs were stimulated with inactivated HIV-1 as above for 16 hours, washed and labelled with the antibodies. Cells were then analysed using a FACScalibur™ flow cytometer and data. analysed using Cell-Quest software. C) Flow cytometric detection of HIV-1 specific CD69+/CD4+ T cells carried out as in B).

FIG. 23 shows a diagram of a system used to carry out the instructions encoded by the storage medium of FIGS. 28 and 29.

FIG. 24 depicts a flow diagram showing an embodiment of a method for designing synthetic polynucleotide and synthetic polypeptides of the invention.

FIG. 25 shows an algorithm, which inter alia utilises the steps of the method shown in FIG. 24.

FIG. 26 shows an example of applying the algorithm of FIG. 25 to an input consensus polyprotein sequence of Hepatitis C1a to execute the segmentation of the polyprotein sequence, the rearrangement of the segments, the linkage of the rearranged segments and the outputting of synthetic polynucleotide and polypeptide sequences for the preparation of Savines for treating and/or preventing Hepatitis C infection.

FIG. 27 illustrates an example of applying the algorithm of FIG. 25 to input consensus melanocyte differentiation antigens (gp100, MART, TRP-1, Tyros, Trp-2, MC1R, MUC1F and MUC1R) and to consensus melanoma specific antigens (BAGE, GAGE-1, gp100In4, MAGE-1, MAGE-3, PRAME, TRP2IN2, NYNSO1a, NYNSO1b and LAGE1) to facilitate segmentation of those sequences, to rearrange the segments, to link the rearranged segments and to synthetic polynucleotide and polypeptide sequences for the preparation of Savines for treating and/or preventing melanoma.

FIG. 28 shows a cross section of a magnetic storage medium.

FIG. 29 shows a cross section of an optically readable data storage medium.

FIG. 30 shows six HIV Savine cassette sequences (A1 [SEQ ID NO: 393], A2 [SEQ ID NO: 399], B1[SEQ ID NO: 395], B2 [SEQ ID NO: 401], C1 [SEQ ID NO: 397] and C2 [SEQ ID NO: 403]). A1, B1 and C1 can be joined together using, for example, convenient restriction enzyme sites provided at the ends of each cassette to construct an embodiment of a full length HIV Savine [SEQ ID NO: 405]. A2, B2 and C2 can also be joined together to provide another embodiment of a full length HIV Savine with 350 aa mutations common in major HIV clades. The cassettes A/B/C can be joined into single constructs using specific restriction enzyme sites incorporated after the start codon or before the stop codon in the cassettes

BRIEF DESCRIPTION OF THE SEQUENCES: SUMMARY TABLE

TABLE A SEQUENCE ID NUMBER SEQUENCE Length SEQ ID NO: 1 GAG consensus polypeptide 499 aa SEQ ID NO: 2 POL consensus polypeptide 995 aa SEQ ID NO: 3 VIF consensus polypeptide 192 aa SEQ ID NO: 4 VPR consensus polypeptide 96 aa SEQ ID NO: 5 TAT consensus polypeptide 102 aa SEQ ID NO: 6 REV consensus polypeptide 123 aa SEQ ID NO: 7 VPU consensus polypeptide 81 aa SEQ ID NO: 8 ENV consensus polypeptide 651 aa SEQ ID NO: 9 NEF consensus polypeptide 206 aa SEQ ID NO: 10 GAG segment 1 90 nts SEQ ID NO: 11 Polypeptide encoded by SEQ ID NO: 10 30 aa SEQ ID NO: 12 GAG segment 2 90 nts SEQ ID NO: 13 Polypeptide encoded by SEQ ID NO: 12 30 aa SEQ ID NO: 14 GAG segment 3 90 nts SEQ ID NO: 15 Polypeptide encoded by SEQ ID NO: 14 30 aa SEQ ID NO: 16 GAG segment 4 90 nts SEQ ID NO: 17 Polypeptide encoded by SEQ ID NO: 16 30 aa SEQ ID NO: 18 GAG segment 5 90 nts SEQ ID NO: 19 Polypeptide encoded by SEQ ID NO: 18 30 aa SEQ ID NO: 20 GAG segment 6 90 nts SEQ ID NO: 21 Polypeptide encoded by SEQ ID NO: 20 30 aa SEQ ID NO: 22 GAG segment 7 90 nts SEQ ID NO: 23 Polypeptide encoded by SEQ ID NO: 22 30 aa SEQ ID NO: 24 GAG segment 8 90 nts SEQ ID NO: 25 Polypeptide encoded by SEQ ID NO: 24 30 aa SEQ ID NO: 26 GAG segment 9 90 nts SEQ ID NO: 27 Polypeptide encoded by SEQ ID NO: 26 30 aa SEQ ID NO: 28 GAG segment 10 90 nts SEQ ID NO: 29 Polypeptide encoded by SEQ ID NO: 28 30 aa SEQ ID NO: 30 GAG segment 11 90 nts SEQ ID NO: 31 Polypeptide encoded by SEQ ID NO: 30 30 aa SEQ ID NO: 32 GAG segment 12 90 nts SEQ ID NO: 33 Polypeptide encoded by SEQ ID NO: 32 30 aa SEQ ID NO: 34 GAG segment 13 90 nts SEQ ID NO: 35 Polypeptide encoded by SEQ ID NO: 34 30 aa SEQ ID NO: 36 GAG segment 14 90 nts SEQ ID NO: 37 Polypeptide encoded by SEQ ID NO: 36 30 aa SEQ ID NO: 38 GAG segment 15 90 nts SEQ ID NO: 39 Polypeptide encoded by SEQ ID NO: 38 30 aa SEQ ID NO: 40 GAG segment 16 90 nts SEQ ID NO: 41 Polypeptide encoded by SEQ ID NO: 40 30 aa SEQ ID NO: 42 GAG segment 17 90 nts SEQ ID NO: 43 Polypeptide encoded by SEQ ID NO: 42 30 aa SEQ ID NO: 44 GAG segment 18 90 nts SEQ ID NO: 45 Polypeptide encoded by SEQ ID NO: 44 30 aa SEQ ID NO: 46 GAG segment 19 90 nts SEQ ID NO: 47 Polypeptide encoded by SEQ ID NO: 46 30 aa SEQ ID NO: 48 GAG segment 20 90 nts SEQ ID NO: 49 Polypeptide encoded by SEQ ID NO: 48 30 aa SEQ ID NO: 50 GAG segment 21 90 nts SEQ ID NO: 51 Polypeptide encoded by SEQ ID NO: 50 30 aa SEQ ID NO: 52 GAG segment 22 90 nts SEQ ID NO: 53 Polypeptide encoded by SEQ ID NO: 52 30 aa SEQ ID NO: 54 GAG segment 23 90 nts SEQ ID NO: 55 Polypeptide encoded by SEQ ID NO: 54 30 aa SEQ ID NO: 56 GAG segment 24 90 nts SEQ ID NO: 57 Polypeptide encoded by SEQ ID NO: 56 30 aa SEQ ID NO: 58 GAG segment 25 90 nts SEQ ID NO: 59 Polypeptide encoded by SEQ ID NO: 58 30 aa SEQ ID NO: 60 GAG segment 26 90 nts SEQ ID NO: 61 Polypeptide encoded by SEQ ID NO: 60 30 aa SEQ ID NO: 62 GAG segment 27 90 nts SEQ ID NO: 63 Polypeptide encoded by SEQ ID NO: 62 30 aa SEQ ID NO: 64 GAG segment 28 90 nts SEQ ID NO: 65 Polypeptide encoded by SEQ ID NO: 64 30 aa SEQ ID NO: 66 GAG segment 29 90 nts SEQ ID NO: 67 Polypeptide encoded by SEQ ID NO: 66 30 aa SEQ ID NO: 68 GAG segment 30 90 nts SEQ ID NO: 69 Polypeptide encoded by SEQ ID NO: 68 30 aa SEQ ID NO: 70 GAG segment 31 90 nts SEQ ID NO: 71 Polypeptide encoded by SEQ ID NO: 70 30 aa SEQ ID NO: 72 GAG segment 32 90 nts SEQ ID NO: 73 Polypeptide encoded by SEQ ID NO: 72 30 aa SEQ ID NO: 74 GAG segment 33 57 nts SEQ ID NO: 75 Polypeptide encoded by SEQ ID NO: 74 19 aa SEQ ID NO: 76 POL segment 1 90 nts SEQ ID NO: 77 Polypeptide encoded by SEQ ID NO: 76 30 aa SEQ ID NO: 78 POL segment 2 90 nts SEQ ID NO: 79 Polypeptide encoded by SEQ ID NO: 78 30 aa SEQ ID NO: 80 POL segment 3 90 nts SEQ ID NO: 81 Polypeptide encoded by SEQ ID NO: 80 30 aa SEQ ID NO: 82 POL segment 4 90 nts SEQ ID NO: 83 Polypeptide encoded by SEQ ID NO: 82 30 aa SEQ ID NO: 84 POL segment 5 90 nts SEQ ID NO: 85 Polypeptide encoded by SEQ ID NO: 84 30 aa SEQ ID NO: 86 POL segment 6 90 nts SEQ ID NO: 87 Polypeptide encoded by SEQ ID NO: 86 30 aa SEQ ID NO: 88 POL segment 7 90 nts SEQ ID NO: 89 Polypeptide encoded by SEQ ID NO: 88 30 aa SEQ ID NO: 90 POL segment 8 90 nts SEQ ID NO: 91 Polypeptide encoded by SEQ ID NO: 90 30 aa SEQ ID NO: 92 POL segment 9 90 nts SEQ ID NO: 93 Polypeptide encoded by SEQ ID NO: 92 30 aa SEQ ID NO: 94 POL segment 10 90 nts SEQ ID NO: 95 Polypeptide encoded by SEQ ID NO: 94 30 aa SEQ ID NO: 96 POL segment 11 90 nts SEQ ID NO: 97 Polypeptide encoded by SEQ ID NO: 96 30 aa SEQ ID NO: 98 POL segment 12 90 nts SEQ ID NO: 99 Polypeptide encoded by SEQ ID NO: 98 30 aa SEQ ID NO: 100 POL segment 13 90 nts SEQ ID NO: 101 Polypeptide encoded by SEQ ID NO: 100 30 aa SEQ ID NO: 102 POL segment 14 90 nts SEQ ID NO: 103 Polypeptide encoded by SEQ ID NO: 102 30 aa SEQ ID NO: 104 POL segment 15 90 nts SEQ ID NO: 105 Polypeptide encoded by SEQ ID NO: 104 30 aa SEQ ID NO: 106 POL segment 16 90 nts SEQ ID NO: 107 Polypeptide encoded by SEQ ID NO: 106 30 aa SEQ ID NO: 108 POL segment 17 90 nts SEQ ID NO: 109 Polypeptide encoded by SEQ ID NO: 108 30 aa SEQ ID NO: 110 POL segment 18 90 nts SEQ ID NO: 111 Polypeptide encoded by SEQ ID NO: 110 30 aa SEQ ID NO: 112 POL segment 19 90 nts SEQ ID NO: 113 Polypeptide encoded by SEQ ID NO: 112 30 aa SEQ ID NO: 114 POL segment 20 90 nts SEQ ID NO: 115 Polypeptide encoded by SEQ ID NO: 114 30 aa SEQ ID NO: 116 POL segment 21 90 nts SEQ ID NO: 117 Polypeptide encoded by SEQ ID NO: 116 30 aa SEQ ID NO: 118 POL segment 22 90 nts SEQ ID NO: 119 Polypeptide encoded by SEQ ID NO: 118 30 aa SEQ ID NO: 120 POL segment 23 90 nts SEQ ID NO: 121 Polypeptide encoded by SEQ ID NO: 120 30 aa SEQ ID NO: 122 POL segment 24 90 nts SEQ ID NO: 123 Polypeptide encoded by SEQ ID NO: 122 30 aa SEQ ID NO: 124 POL segment 25 90 nts SEQ ID NO: 125 Polypeptide encoded by SEQ ID NO: 124 30 aa SEQ ID NO: 126 POL segment 26 90 nts SEQ ID NO: 127 Polypeptide encoded by SEQ ID NO: 126 30 aa SEQ ID NO: 128 POL segment 27 90 nts SEQ ID NO: 129 Polypeptide encoded by SEQ ID NO: 128 30 aa SEQ ID NO: 130 POL segment 28 90 nts SEQ ID NO: 131 Polypeptide encoded by SEQ ID NO: 130 30 aa SEQ ID NO: 132 POL segment 29 90 nts SEQ ID NO: 133 Polypeptide encoded by SEQ ID NO: 132 30 aa SEQ ID NO: 134 POL segment 30 90 nts SEQ ID NO: 135 Polypeptide encoded by SEQ ID NO: 134 30 aa SEQ ID NO: 136 POL segment 31 90 nts SEQ ID NO: 137 Polypeptide encoded by SEQ ID NO: 136 30 aa SEQ ID NO: 138 POL segment 32 90 nts SEQ ID NO: 139 Polypeptide encoded by SEQ ID NO: 138 30 aa SEQ ID NO: 140 POL segment 33 90 nts SEQ ID NO: 141 Polypeptide encoded by SEQ ID NO: 140 30 aa SEQ ID NO: 142 POL segment 34 90 nts SEQ ID NO: 143 Polypeptide encoded by SEQ ID NO: 142 30 aa SEQ ID NO: 144 POL segment 35 90 nts SEQ ID NO: 145 Polypeptide encoded by SEQ ID NO: 144 30 aa SEQ ID NO: 146 POL segment 36 90 nts SEQ ID NO: 147 Polypeptide encoded by SEQ ID NO: 146 30 aa SEQ ID NO: 148 POL segment 37 90 nts SEQ ID NO: 149 Polypeptide encoded by SEQ ID NO: 148 30 aa SEQ ID NO: 150 POL segment 38 90 nts SEQ ID NO: 151 Polypeptide encoded by SEQ ID NO: 150 30 aa SEQ ID NO: 152 POL segment 39 90 nts SEQ ID NO: 153 Polypeptide encoded by SEQ ID NO: 152 30 aa SEQ ID NO: 154 POL segment 40 90 nts SEQ ID NO: 155 Polypeptide encoded by SEQ ID NO: 154 30 aa SEQ ID NO: 156 POL segment 41 90 nts SEQ ID NO: 157 Polypeptide encoded by SEQ ID NO: 156 30 aa SEQ ID NO: 158 POL segment 42 90 nts SEQ ID NO: 159 Polypeptide encoded by SEQ ID NO: 158 30 aa SEQ ID NO: 160 POL segment 43 90 nts SEQ ID NO: 161 Polypeptide encoded by SEQ ID NO: 160 30 aa SEQ ID NO: 162 POL segment 44 90 nts SEQ ID NO: 163 Polypeptide encoded by SEQ ID NO: 162 30 aa SEQ ID NO: 164 POL segment 45 90 nts SEQ ID NO: 165 Polypeptide encoded by SEQ ID NO: 164 30 aa SEQ ID NO: 166 POL segment 46 90 nts SEQ ID NO: 167 Polypeptide encoded by SEQ ID NO: 166 30 aa SEQ ID NO: 168 POL segment 47 90 nts SEQ ID NO: 169 Polypeptide encoded by SEQ ID NO: 168 30 aa SEQ ID NO: 170 POL segment 48 90 nts SEQ ID NO: 171 Polypeptide encoded by SEQ ID NO: 170 30 aa SEQ ID NO: 172 POL segment 49 90 nts SEQ ID NO: 173 Polypeptide encoded by SEQ ID NO: 172 30 aa SEQ ID NO: 174 POL segment 50 90 nts SEQ ID NO: 175 Polypeptide encoded by SEQ ID NO: 174 30 aa SEQ ID NO: 176 POL segment 51 90 nts SEQ ID NO: 177 Polypeptide encoded by SEQ ID NO: 176 30 aa SEQ ID NO: 178 POL segment 52 90 nts SEQ ID NO: 179 Polypeptide encoded by SEQ ID NO: 178 30 aa SEQ ID NO: 180 POL segment 53 90 nts SEQ ID NO: 181 Polypeptide encoded by SEQ ID NO: 180 30 aa SEQ ID NO: 182 POL segment 54 90 nts SEQ ID NO: 183 Polypeptide encoded by SEQ ID NO: 182 30 aa SEQ ID NO: 184 POL segment 55 90 nts SEQ ID NO: 185 Polypeptide encoded by SEQ ID NO: 184 30 aa SEQ ID NO: 186 POL segment 56 90 nts SEQ ID NO: 187 Polypeptide encoded by SEQ ID NO: 186 30 aa SEQ ID NO: 188 POL segment 57 90 nts SEQ ID NO: 189 Polypeptide encoded by SEQ ID NO: 188 30 aa SEQ ID NO: 190 POL segment 58 90 nts SEQ ID NO: 191 Polypeptide encoded by SEQ ID NO: 190 30 aa SEQ ID NO: 192 POL segment 59 90 nts SEQ ID NO: 193 Polypeptide encoded by SEQ ID NO: 192 30 aa SEQ ID NO: 194 POL segment 60 90 nts SEQ ID NO: 195 Polypeptide encoded by SEQ ID NO: 194 30 aa SEQ ID NO: 196 POL segment 61 90 nts SEQ ID NO: 197 Polypeptide encoded by SEQ ID NO: 196 30 aa SEQ ID NO: 198 POL segment 62 90 nts SEQ ID NO: 199 Polypeptide encoded by SEQ ID NO: 198 30 aa SEQ ID NO: 200 POL segment 63 90 nts SEQ ID NO: 201 Polypeptide encoded by SEQ ID NO: 200 30 aa SEQ ID NO: 202 POL segment 64 90 nts SEQ ID NO: 203 Polypeptide encoded by SEQ ID NO: 202 30 aa SEQ ID NO: 204 POL segment 65 90 nts SEQ ID NO: 205 Polypeptide encoded by SEQ ID NO: 204 30 aa SEQ ID NO: 206 POL segment 66 60 nts SEQ ID NO: 207 Polypeptide encoded by SEQ ID NO: 206 20 aa SEQ ID NO: 208 VIF segment 1 90 nts SEQ ID NO: 209 Polypeptide encoded by SEQ ID NO: 208 30 aa SEQ ID NO: 210 VIF segment 2 90 nts SEQ ID NO: 211 Polypeptide encoded by SEQ ID NO: 210 30 aa SEQ ID NO: 212 VIF segment 3 90 nts SEQ ID NO: 213 Polypeptide encoded by SEQ ID NO: 212 30 aa SEQ ID NO: 214 VIF segment 4 90 nts SEQ ID NO: 215 Polypeptide encoded by SEQ ID NO: 214 30 aa SEQ ID NO: 216 VIF segment 5 90 nts SEQ ID NO: 217 Polypeptide encoded by SEQ ID NO: 216 30 aa SEQ ID NO: 218 VIF segment 6 90 nts SEQ ID NO: 219 Polypeptide encoded by SEQ ID NO: 218 30 aa SEQ ID NO: 220 VIF segment 7 90 nts SEQ ID NO: 221 Polypeptide encoded by SEQ ID NO: 220 30 aa SEQ ID NO: 222 VIF segment 8 90 nts SEQ ID NO: 223 Polypeptide encoded by SEQ ID NO: 222 30 aa SEQ ID NO: 224 VIF segment 9 90 nts SEQ ID NO: 225 Polypeptide encoded by SEQ ID NO: 224 30 aa SEQ ID NO: 226 VIF segment 10 90 nts SEQ ID NO: 227 Polypeptide encoded by SEQ ID NO: 226 30 aa SEQ ID NO: 228 VIF segment 11 90 nts SEQ ID NO: 229 Polypeptide encoded by SEQ ID NO: 228 30 aa SEQ ID NO: 230 VIF segment 12 81 nts SEQ ID NO: 231 Polypeptide encoded by SEQ ID NO: 230 27 aa SEQ ID NO: 232 VPR segment 1 90 nts SEQ ID NO: 233 Polypeptide encoded by SEQ ID NO: 232 30 aa SEQ ID NO: 234 VPR segment 2 90 nts SEQ ID NO: 235 Polypeptide encoded by SEQ ID NO: 234 30 aa SEQ ID NO: 236 VPR segment 3 90 nts SEQ ID NO: 237 Polypeptide encoded by SEQ ID NO: 236 30 aa SEQ ID NO: 238 VPR segment 4 90 nts SEQ ID NO: 239 Polypeptide encoded by SEQ ID NO: 238 30 aa SEQ ID NO: 240 VPR segment 5 90 nts SEQ ID NO: 241 Polypeptide encoded by SEQ ID NO: 240 30 aa SEQ ID NO: 242 VPR segment 6 63 nts SEQ ID NO: 243 Polypeptide encoded by SEQ ID NO: 242 21 aa SEQ ID NO: 244 TAT segment 1 90 nts SEQ ID NO: 245 Polypeptide encoded by SEQ ID NO: 244 30 aa SEQ ID NO: 246 TAT segment 2 90 nts SEQ ID NO: 247 Polypeptide encoded by SEQ ID NO: 246 30 aa SEQ ID NO: 248 TAT segment 3 90 nts SEQ ID NO: 249 Polypeptide encoded by SEQ ID NO: 248 30 aa SEQ ID NO: 250 TAT segment 4 90 nts SEQ ID NO: 251 Polypeptide encoded by SEQ ID NO: 250 30 aa SEQ ID NO: 252 TAT segment 5 90 nts SEQ ID NO: 253 Polypeptide encoded by SEQ ID NO: 252 30 aa SEQ ID NO: 254 TAT segment 6 81 nts SEQ ID NO: 255 Polypeptide encoded by SEQ ID NO: 254 27 aa SEQ ID NO: 256 REV segment 1 90 nts SEQ ID NO: 257 Polypeptide encoded by SEQ ID NO: 256 30 aa SEQ ID NO: 258 REV segment 2 90 nts SEQ ID NO: 259 Polypeptide encoded by SEQ ID NO: 258 30 aa SEQ ID NO: 260 REV segment 3 90 nts SEQ ID NO: 261 Polypeptide encoded by SEQ ID NO: 260 30 aa SEQ ID NO: 262 REV segment 4 90 nts SEQ ID NO: 263 Polypeptide encoded by SEQ ID NO: 262 30 aa SEQ ID NO: 264 REV segment 5 90 nts SEQ ID NO: 265 Polypeptide encoded by SEQ ID NO: 264 30 aa SEQ ID NO: 266 REV segment 6 90 nts SEQ ID NO: 267 Polypeptide encoded by SEQ ID NO: 266 30 aa SEQ ID NO: 268 REV segment 7 90 nts SEQ ID NO: 269 Polypeptide encoded by SEQ ID NO: 268 30 aa SEQ ID NO: 270 REV segment 8 54 nts SEQ ID NO: 271 Polypeptide encoded by SEQ ID NO: 270 18 aa SEQ ID NO: 272 VPU segment 1 90 nts SEQ ID NO: 273 Polypeptide encoded by SEQ ID NO: 272 30 aa SEQ ID NO: 274 VPU segment 2 90 nts SEQ ID NO: 275 Polypeptide encoded by SEQ ID NO: 274 30 aa SEQ ID NO: 276 VPU segment 3 90 nts SEQ ID NO: 277 Polypeptide encoded by SEQ ID NO: 276 30 aa SEQ ID NO: 278 VPU segment 4 90 nts SEQ ID NO: 279 Polypeptide encoded by SEQ ID NO: 278 30 aa SEQ ID NO: 280 VPU segment 5 63 nts SEQ ID NO: 281 Polypeptide encoded by SEQ ID NO: 280 21 aa SEQ ID NO: 282 ENV segment 1 90 nts SEQ ID NO: 283 Polypeptide encoded by SEQ ID NO: 282 30 aa SEQ ID NO: 284 ENV segment 2 90 nts SEQ ID NO: 285 Polypeptide encoded by SEQ ID NO: 284 30 aa SEQ ID NO: 286 ENV segment 3 90 nts SEQ ID NO: 287 Polypeptide encoded by SEQ ID NO: 286 30 aa SEQ ID NO: 288 ENV segment 4 90 nts SEQ ID NO: 289 Polypeptide encoded by SEQ ID NO: 288 30 aa SEQ ID NO: 290 ENV segment 5 90 nts SEQ ID NO: 291 Polypeptide encoded by SEQ ID NO: 290 30 aa SEQ ID NO: 292 ENV segment 6 90 nts SEQ ID NO: 293 Polypeptide encoded by SEQ ID NO: 292 30 aa SEQ ID NO: 294 ENV segment 7 90 nts SEQ ID NO: 295 Polypeptide encoded by SEQ ID NO: 294 30 aa SEQ ID NO: 296 ENV segment 8 90 nts SEQ ID NO: 297 Polypeptide encoded by SEQ ID NO: 296 30 aa SEQ ID NO: 298 ENV segment 9 57 nts SEQ ID NO: 299 Polypeptide encoded by SEQ ID NO: 298 19 aa SEQ ID NO: 300 GAP A segment 1 90 nts SEQ ID NO: 301 Polypeptide encoded by SEQ ID NO: 300 30 aa SEQ ID NO: 302 GAP A segment 2 90 nts SEQ ID NO: 303 Polypeptide encoded by SEQ ID NO: 302 30 aa SEQ ID NO: 304 GAP A segment 3 90 nts SEQ ID NO: 305 Polypeptide encoded by SEQ ID NO: 304 30 aa SEQ ID NO: 306 GAP A segment 4 90 nts SEQ ID NO: 307 Polypeptide encoded by SEQ ID NO: 306 30 aa SEQ ID NO: 308 GAP A segment 5 90 nts SEQ ID NO: 309 Polypeptide encoded by SEQ ID NO: 308 30 aa SEQ ID NO: 310 GAP A segment 6 90 nts SEQ ID NO: 311 Polypeptide encoded by SEQ ID NO: 310 30 aa SEQ ID NO: 312 GAP A segment 7 75 nts SEQ ID NO: 313 Polypeptide encoded by SEQ ID NO: 312 25 nts SEQ ID NO: 314 GAP B segment 1 90 nts SEQ ID NO: 315 Polypeptide encoded by SEQ ID NO: 314 30 aa SEQ ID NO: 316 GAP B segment 2 90 nts SEQ ID NO: 317 Polypeptide encoded by SEQ ID NO: 316 30 aa SEQ ID NO: 318 GAP B segment 3 90 nts SEQ ID NO: 319 Polypeptide encoded by SEQ ID NO: 318 30 aa SEQ ID NO: 320 GAP B segment 4 90 nts SEQ ID NO: 321 Polypeptide encoded by SEQ ID NO: 320 30 aa SEQ ID NO: 322 GAP B segment 5 90 nts SEQ ID NO: 323 Polypeptide encoded by SEQ ID NO: 322 30 aa SEQ ID NO: 324 GAP B segment 6 90 nts SEQ ID NO: 325 Polypeptide encoded by SEQ ID NO: 324 30 aa SEQ ID NO: 326 GAP B segment 7 90 nts SEQ ID NO: 327 Polypeptide encoded by SEQ ID NO: 326 30 aa SEQ ID NO: 328 GAP B segment 8 90 nts SEQ ID NO: 329 Polypeptide encoded by SEQ ID NO: 328 30 aa SEQ ID NO: 330 GAP B segment 9 90 nts SEQ ID NO: 331 Polypeptide encoded by SEQ ID NO: 330 30 aa SEQ ID NO: 332 GAP B segment 10 90 nts SEQ ID NO: 333 Polypeptide encoded by SEQ ID NO: 332 30 aa SEQ ID NO: 334 GAP B segment 11 90 nts SEQ ID NO: 335 Polypeptide encoded by SEQ ID NO: 334 30 aa SEQ ID NO: 336 GAP B segment 12 90 nts SEQ ID NO: 337 Polypeptide encoded by SEQ ID NO: 336 30 aa SEQ ID NO: 338 GAP B segment 13 90 nts SEQ ID NO: 339 Polypeptide encoded by SEQ ID NO: 338 30 aa SEQ ID NO: 340 GAP B segment 14 90 nts SEQ ID NO: 341 Polypeptide encoded by SEQ ID NO: 340 30 aa SEQ ID NO: 342 GAP B segment 15 90 nts SEQ ID NO: 343 Polypeptide encoded by SEQ ID NO: 342 30 aa SEQ ID NO: 344 GAP B segment 16 90 nts SEQ ID NO: 345 Polypeptide encoded by SEQ ID NO: 344 30 aa SEQ ID NO: 346 GAP B segment 17 90 nts SEQ ID NO: 347 Polypeptide encoded by SEQ ID NO: 346 30 aa SEQ ID NO: 348 GAP B segment 18 90 nts SEQ ID NO: 349 Polypeptide encoded by SEQ ID NO: 348 30 aa SEQ ID NO: 350 GAP B segment 19 90 nts SEQ ID NO: 351 Polypeptide encoded by SEQ ID NO: 350 30 aa SEQ ID NO: 352 GAP B segment 20 90 nts SEQ ID NO: 353 Polypeptide encoded by SEQ ID NO: 352 30 aa SEQ ID NO: 354 GAP B segment 21 90 nts SEQ ID NO: 355 Polypeptide encoded by SEQ ID NO: 354 30 aa SEQ ID NO: 356 GAP B segment 22 90 nts SEQ ID NO: 357 Polypeptide encoded by SEQ ID NO: 356 30 aa SEQ ID NO: 358 GAP B segment 23 90 nts SEQ ID NO: 359 Polypeptide encoded by SEQ ID NO: 358 30 aa SEQ ID NO: 360 GAP B segment 24 90 nts SEQ ID NO: 361 Polypeptide encoded by SEQ ID NO: 360 30 aa SEQ ID NO: 362 GAP B segment 25 90 nts SEQ ID NO: 363 Polypeptide encoded by SEQ ID NO: 362 30 aa SEQ ID NO: 364 GAP B segment 26 66 nts SEQ ID NO: 365 Polypeptide encoded by SEQ ID NO: 364 22 aa SEQ ID NO: 366 NEF segment 1 90 nts SEQ ID NO: 367 Polypeptide encoded by SEQ ID NO: 366 30 aa SEQ ID NO: 368 NEF segment 2 90 nts SEQ ID NO: 369 Polypeptide encoded by SEQ ID NO: 368 30 aa SEQ ID NO: 370 NEF segment 3 90 nts SEQ ID NO: 371 Polypeptide encoded by SEQ ID NO: 370 30 aa SEQ ID NO: 372 NEF segment 4 90 nts SEQ ID NO: 373 Polypeptide encoded by SEQ ID NO: 372 30 aa SEQ ID NO: 374 NEF segment 5 90 nts SEQ ID NO: 375 Polypeptide encoded by SEQ ID NO: 374 30 aa SEQ ID NO: 376 NEF segment 6 90 nts SEQ ID NO: 377 Polypeptide encoded by SEQ ID NO: 376 30 aa SEQ ID NO: 378 NEF segment 7 90 nts SEQ ID NO: 379 Polypeptide encoded by SEQ ID NO: 378 30 aa SEQ ID NO: 380 NEF segment 8 90 nts SEQ ID NO: 381 Polypeptide encoded by SEQ ID NO: 380 30 aa SEQ ID NO: 382 NEF segment 9 90 nts SEQ ID NO: 383 Polypeptide encoded by SEQ ID NO: 382 30 aa SEQ ID NO: 384 NEF segment 10 90 nts SEQ ID NO: 385 Polypeptide encoded by SEQ ID NO: 384 30 aa SEQ ID NO: 386 NEF segment 11 90 nts SEQ ID NO: 387 Polypeptide encoded by SEQ ID NO: 386 30 aa SEQ ID NO: 388 NEF segment 12 90 nts SEQ ID NO: 389 Polypeptide encoded by SEQ ID NO: 388 30 aa SEQ ID NO: 390 NEF segment 13 78 nts SEQ ID NO: 391 Polypeptide encoded by SEQ ID NO: 390 26 aa SEQ ID NO: 392 HIV Cassette A1 5703 nts SEQ ID NO: 393 Polypeptide encoded by SEQ ID NO: 392 1896 aa SEQ ID NO: 394 HIV Cassette B1 5685 nts SEQ ID NO: 395 Polypeptide encoded by SEQ ID NO: 394 1890 aa SEQ ID NO: 396 HIV Cassette C1 5925 nts SEQ ID NO: 397 Polypeptide encoded by SEQ ID NO: 396 1967 aa SEQ ID NO: 398 HIV Cassette A2 5703 nts SEQ ID NO: 399 Polypeptide encoded by SEQ ID NO: 398 1896 aa SEQ ID NO: 400 HIV Cassette B2 5685 nts SEQ ID NO: 401 Polypeptide encoded by SEQ ID NO: 400 1890 aa SEQ ID NO: 402 HIV Cassette C2 5925 nts SEQ ID NO: 403 Polypeptide encoded by SEQ ID NO: 402 1967 aa SEQ ID NO: 404 HIV complete Savine 17244 nts SEQ ID NO: 405 Polypeptide encoded by SEQ ID NO: 404 5747 aa SEQ ID NO: 406 HepC1a consensus polyprotein sequence 3011 aa SEQ ID NO: 407 HepC1a segment 1 90 nts SEQ ID NO: 408 Polypeptide encoded by SEQ ID NO: 407 30 aa SEQ ID NO: 409 HepC1a segment 2 90 nts SEQ ID NO: 410 Polypeptide encoded by SEQ ID NO: 409 30 aa SEQ ID NO: 411 HepC1a segment 3 90 nts SEQ ID NO: 412 Polypeptide encoded by SEQ ID NO: 411 30 aa SEQ ID NO: 413 HepC1a segment 4 90 nts SEQ ID NO: 414 Polypeptide encoded by SEQ ID NO: 413 30 aa SEQ ID NO: 415 HepC1a segment 5 90 nts SEQ ID NO: 416 Polypeptide encoded by SEQ ID NO: 415 30 aa SEQ ID NO: 417 HepC1a segment 6 90 nts SEQ ID NO: 418 Polypeptide encoded by SEQ ID NO: 417 30 aa SEQ ID NO: 419 HepC1a segment 7 90 nts SEQ ID NO: 420 Polypeptide encoded by SEQ ID NO: 419 30 aa SEQ ID NO: 421 HepC1a segment 8 90 nts SEQ ID NO: 422 Polypeptide encoded by SEQ ID NO: 421 30 aa SEQ ID NO: 423 HepC1a segment 9 90 nts SEQ ID NO: 424 Polypeptide encoded by SEQ ID NO: 423 30 aa SEQ ID NO: 425 HepC1a segment 10 90 nts SEQ ID NO: 426 Polypeptide encoded by SEQ ID NO: 425 30 aa SEQ ID NO: 427 HepC1a segment 11 90 nts SEQ ID NO: 428 Polypeptide encoded by SEQ ID NO: 427 30 aa SEQ ID NO: 429 HepC1a segment 12 90 nts SEQ ID NO: 430 Polypeptide encoded by SEQ ID NO: 429 30 aa SEQ ID NO: 431 HepC1a segment 13 90 nts SEQ ID NO: 432 Polypeptide encoded by SEQ ID NO: 431 30 aa SEQ ID NO: 433 HepC1a segment 14 90 nts SEQ ID NO: 434 Polypeptide encoded by SEQ ID NO: 433 30 aa SEQ ID NO: 435 HepC1a segment 15 90 nts SEQ ID NO: 436 Polypeptide encoded by SEQ ID NO: 435 30 aa SEQ ID NO: 437 HepC1a segment 16 90 nts SEQ ID NO: 438 Polypeptide encoded by SEQ ID NO: 437 30 aa SEQ ID NO: 439 HepC1a segment 17 90 nts SEQ ID NO: 440 Polypeptide encoded by SEQ ID NO: 439 30 aa SEQ ID NO: 441 HepC1a segment 18 90 nts SEQ ID NO: 442 Polypeptide encoded by SEQ ID NO: 441 30 aa SEQ ID NO: 443 HepC1a segment 19 90 nts SEQ ID NO: 444 Polypeptide encoded by SEQ ID NO: 443 30 aa SEQ ID NO: 445 HepC1a segment 20 90 nts SEQ ID NO: 446 Polypeptide encoded by SEQ ID NO: 445 30 aa SEQ ID NO: 447 HepC1a segment 21 90 nts SEQ ID NO: 448 Polypeptide encoded by SEQ ID NO: 447 30 aa SEQ ID NO: 449 HepC1a segment 22 90 nts SEQ ID NO: 450 Polypeptide encoded by SEQ ID NO: 449 30 aa SEQ ID NO: 451 HepC1a segment 23 90 nts SEQ ID NO: 452 Polypeptide encoded by SEQ ID NO: 451 30 aa SEQ ID NO: 453 HepC1a segment 24 90 nts SEQ ID NO: 454 Polypeptide encoded by SEQ ID NO: 453 30 aa SEQ ID NO: 455 HepC1a segment 25 90 nts SEQ ID NO: 456 Polypeptide encoded by SEQ ID NO: 455 30 aa SEQ ID NO: 457 HepC1a segment 26 90 nts SEQ ID NO: 458 Polypeptide encoded by SEQ ID NO: 457 30 aa SEQ ID NO: 459 HepC1a segment 27 90 nts SEQ ID NO: 460 Polypeptide encoded by SEQ ID NO: 459 30 aa SEQ ID NO: 461 HepC1a segment 28 90 nts SEQ ID NO: 462 Polypeptide encoded by SEQ ID NO: 461 30 aa SEQ ID NO: 463 HepC1a segment 29 90 nts SEQ ID NO: 464 Polypeptide encoded by SEQ ID NO: 463 30 aa SEQ ID NO: 465 HepC1a segment 30 90 nts SEQ ID NO: 466 Polypeptide encoded by SEQ ID NO: 465 30 aa SEQ ID NO: 467 HepC1a segment 31 90 nts SEQ ID NO: 468 Polypeptide encoded by SEQ ID NO: 467 30 aa SEQ ID NO: 469 HepC1a segment 32 90 nts SEQ ID NO: 470 Polypeptide encoded by SEQ ID NO: 469 30 aa SEQ ID NO: 471 HepC1a segment 33 90 nts SEQ ID NO: 472 Polypeptide encoded by SEQ ID NO: 471 30 aa SEQ ID NO: 473 HepC1a segment 34 90 nts SEQ ID NO: 474 Polypeptide encoded by SEQ ID NO: 473 30 aa SEQ ID NO: 475 HepC1a segment 35 90 nts SEQ ID NO: 476 Polypeptide encoded by SEQ ID NO: 475 30 aa SEQ ID NO: 477 HepC1a segment 36 90 nts SEQ ID NO: 478 Polypeptide encoded by SEQ ID NO: 477 30 aa SEQ ID NO: 479 HepC1a segment 37 90 nts SEQ ID NO: 480 Polypeptide encoded by SEQ ID NO: 479 30 aa SEQ ID NO: 481 HepC1a segment 38 90 nts SEQ ID NO: 482 Polypeptide encoded by SEQ ID NO: 481 30 aa SEQ ID NO: 483 HepC1a segment 39 90 nts SEQ ID NO: 484 Polypeptide encoded by SEQ ID NO: 483 30 aa SEQ ID NO: 485 HepC1a segment 40 90 nts SEQ ID NO: 486 Polypeptide encoded by SEQ ID NO: 485 30 aa SEQ ID NO: 487 HepC1a segment 41 90 nts SEQ ID NO: 488 Polypeptide encoded by SEQ ID NO: 487 30 aa SEQ ID NO: 489 HepC1a segment 42 90 nts SEQ ID NO: 490 Polypeptide encoded by SEQ ID NO: 489 30 aa SEQ ID NO: 491 HepC1a segment 43 90 nts SEQ ID NO: 492 Polypeptide encoded by SEQ ID NO: 491 30 aa SEQ ID NO: 493 HepC1a segment 44 90 nts SEQ ID NO: 494 Polypeptide encoded by SEQ ID NO: 493 30 aa SEQ ID NO: 495 HepC1a segment 45 90 nts SEQ ID NO: 496 Polypeptide encoded by SEQ ID NO: 495 30 aa SEQ ID NO: 497 HepC1a segment 46 90 nts SEQ ID NO: 498 Polypeptide encoded by SEQ ID NO: 497 30 aa SEQ ID NO: 499 HepC1a segment 47 90 nts SEQ ID NO: 500 Polypeptide encoded by SEQ ID NO: 499 30 aa SEQ ID NO: 501 HepC1a segment 48 90 nts SEQ ID NO: 502 Polypeptide encoded by SEQ ID NO: 501 30 aa SEQ ID NO: 503 HepC1a segment 49 90 nts SEQ ID NO: 504 Polypeptide encoded by SEQ ID NO: 503 30 aa SEQ ID NO: 505 HepC1a segment 50 90 nts SEQ ID NO: 506 Polypeptide encoded by SEQ ID NO: 505 30 aa SEQ ID NO: 507 HepC1a segment 51 90 nts SEQ ID NO: 508 Polypeptide encoded by SEQ ID NO: 507 30 aa SEQ ID NO: 509 HepC1a segment 52 90 nts SEQ ID NO: 510 Polypeptide encoded by SEQ ID NO: 509 30 aa SEQ ID NO: 511 HepC1a segment 53 90 nts SEQ ID NO: 512 Polypeptide encoded by SEQ ID NO: 511 30 aa SEQ ID NO: 513 HepC1a segment 54 90 nts SEQ ID NO: 514 Polypeptide encoded by SEQ ID NO: 513 30 aa SEQ ID NO: 515 HepC1a segment 55 90 nts SEQ ID NO: 516 Polypeptide encoded by SEQ ID NO: 515 30 aa SEQ ID NO: 517 HepC1a segment 56 90 nts SEQ ID NO: 518 Polypeptide encoded by SEQ ID NO: 517 30 aa SEQ ID NO: 519 HepC1a segment 57 90 nts SEQ ID NO: 520 Polypeptide encoded by SEQ ID NO: 519 30 aa SEQ ID NO: 521 HepC1a segment 58 90 nts SEQ ID NO: 522 Polypeptide encoded by SEQ ID NO: 521 30 aa SEQ ID NO: 523 HepC1a segment 59 90 nts SEQ ID NO: 524 Polypeptide encoded by SEQ ID NO: 523 30 aa SEQ ID NO: 525 HepC1a segment 60 90 nts SEQ ID NO: 526 Polypeptide encoded by SEQ ID NO: 525 30 aa SEQ ID NO: 527 HepC1a segment 61 90 nts SEQ ID NO: 528 Polypeptide encoded by SEQ ID NO: 527 30 aa SEQ ID NO: 529 HepC1a segment 62 90 nts SEQ ID NO: 530 Polypeptide encoded by SEQ ID NO: 529 30 aa SEQ ID NO: 531 HepC1a segment 63 90 nts SEQ ID NO: 532 Polypeptide encoded by SEQ ID NO: 531 30 aa SEQ ID NO: 533 HepC1a segment 64 90 nts SEQ ID NO: 534 Polypeptide encoded by SEQ ID NO: 533 30 aa SEQ ID NO: 535 HepC1a segment 65 90 nts SEQ ID NO: 536 Polypeptide encoded by SEQ ID NO: 535 30 aa SEQ ID NO: 537 HepC1a segment 66 90 nts SEQ ID NO: 538 Polypeptide encoded by SEQ ID NO: 537 30 aa SEQ ID NO: 539 HepC1a segment 67 90 nts SEQ ID NO: 540 Polypeptide encoded by SEQ ID NO: 539 30 aa SEQ ID NO: 541 HepC1a segment 68 90 nts SEQ ID NO: 542 Polypeptide encoded by SEQ ID NO: 541 30 aa SEQ ID NO: 543 HepC1a segment 69 90 nts SEQ ID NO: 544 Polypeptide encoded by SEQ ID NO: 543 30 aa SEQ ID NO: 545 HepC1a segment 70 90 nts SEQ ID NO: 546 Polypeptide encoded by SEQ ID NO: 545 30 aa SEQ ID NO: 547 HepC1a segment 71 90 nts SEQ ID NO: 548 Polypeptide encoded by SEQ ID NO: 547 30 aa SEQ ID NO: 549 HepC1a segment 72 90 nts SEQ ID NO: 550 Polypeptide encoded by SEQ ID NO: 549 30 aa SEQ ID NO: 551 HepC1a segment 73 90 nts SEQ ID NO: 552 Polypeptide encoded by SEQ ID NO: 551 30 aa SEQ ID NO: 553 HepC1a segment 74 90 nts SEQ ID NO: 554 Polypeptide encoded by SEQ ID NO: 553 30 aa SEQ ID NO: 555 HepC1a segment 75 90 nts SEQ ID NO: 556 Polypeptide encoded by SEQ ID NO: 555 30 aa SEQ ID NO: 557 HepC1a segment 76 90 nts SEQ ID NO: 558 Polypeptide encoded by SEQ ID NO: 557 30 aa SEQ ID NO: 559 HepC1a segment 77 90 nts SEQ ID NO: 560 Polypeptide encoded by SEQ ID NO: 559 30 aa SEQ ID NO: 561 HepC1a segment 78 90 nts SEQ ID NO: 562 Polypeptide encoded by SEQ ID NO: 561 30 aa SEQ ID NO: 563 HepC1a segment 79 90 nts SEQ ID NO: 564 Polypeptide encoded by SEQ ID NO: 563 30 aa SEQ ID NO: 565 HepC1a segment 80 90 nts SEQ ID NO: 566 Polypeptide encoded by SEQ ID NO: 565 30 aa SEQ ID NO: 567 HepC1a segment 81 90 nts SEQ ID NO: 568 Polypeptide encoded by SEQ ID NO: 567 30 aa SEQ ID NO: 569 HepC1a segment 82 90 nts SEQ ID NO: 570 Polypeptide encoded by SEQ ID NO: 569 30 aa SEQ ID NO: 571 HepC1a segment 83 90 nts SEQ ID NO: 572 Polypeptide encoded by SEQ ID NO: 571 30 aa SEQ ID NO: 573 HepC1a segment 84 90 nts SEQ ID NO: 574 Polypeptide encoded by SEQ ID NO: 573 30 aa SEQ ID NO: 575 HepC1a segment 85 90 nts SEQ ID NO: 576 Polypeptide encoded by SEQ ID NO: 575 30 aa SEQ ID NO: 577 HepC1a segment 86 90 nts SEQ ID NO: 578 Polypeptide encoded by SEQ ID NO: 577 30 aa SEQ ID NO: 579 HepC1a segment 87 90 nts SEQ ID NO: 580 Polypeptide encoded by SEQ ID NO: 579 30 aa SEQ ID NO: 581 HepC1a segment 88 90 nts SEQ ID NO: 582 Polypeptide encoded by SEQ ID NO: 581 30 aa SEQ ID NO: 583 HepC1a segment 89 90 nts SEQ ID NO: 584 Polypeptide encoded by SEQ ID NO: 583 30 aa SEQ ID NO: 585 HepC1a segment 90 90 nts SEQ ID NO: 586 Polypeptide encoded by SEQ ID NO: 585 30 aa SEQ ID NO: 587 HepC1a segment 91 90 nts SEQ ID NO: 588 Polypeptide encoded by SEQ ID NO: 587 30 aa SEQ ID NO: 589 HepC1a segment 92 90 nts SEQ ID NO: 590 Polypeptide encoded by SEQ ID NO: 589 30 aa SEQ ID NO: 591 HepC1a segment 93 90 nts SEQ ID NO: 592 Polypeptide encoded by SEQ ID NO: 591 30 aa SEQ ID NO: 593 HepC1a segment 94 90 nts SEQ ID NO: 594 Polypeptide encoded by SEQ ID NO: 593 30 aa SEQ ID NO: 595 HepC1a segment 95 90 nts SEQ ID NO: 596 Polypeptide encoded by SEQ ID NO: 595 30 aa SEQ ID NO: 597 HepC1a segment 96 90 nts SEQ ID NO: 598 Polypeptide encoded by SEQ ID NO: 597 30 aa SEQ ID NO: 599 HepC1a segment 97 90 nts SEQ ID NO: 600 Polypeptide encoded by SEQ ID NO: 599 30 aa SEQ ID NO: 601 HepC1a segment 98 90 nts SEQ ID NO: 602 Polypeptide encoded by SEQ ID NO: 601 30 aa SEQ ID NO: 603 HepC1a segment 99 90 nts SEQ ID NO: 604 Polypeptide encoded by SEQ ID NO: 603 30 aa SEQ ID NO: 605 HepC1a segment 100 90 nts SEQ ID NO: 606 Polypeptide encoded by SEQ ID NO: 605 30 aa SEQ ID NO: 607 HepC1a segment 101 90 nts SEQ ID NO: 608 Polypeptide encoded by SEQ ID NO: 607 30 aa SEQ ID NO: 609 HepC1a segment 102 90 nts SEQ ID NO: 610 Polypeptide encoded by SEQ ID NO: 609 30 aa SEQ ID NO: 611 HepC1a segment 103 90 nts SEQ ID NO: 612 Polypeptide encoded by SEQ ID NO: 611 30 aa SEQ ID NO: 613 HepC1a segment 104 90 nts SEQ ID NO: 614 Polypeptide encoded by SEQ ID NO: 613 30 aa SEQ ID NO: 615 HepC1a segment 105 90 nts SEQ ID NO: 616 Polypeptide encoded by SEQ ID NO: 615 30 aa SEQ ID NO: 617 HepC1a segment 106 90 nts SEQ ID NO: 618 Polypeptide encoded by SEQ ID NO: 617 30 aa SEQ ID NO: 619 HepC1a segment 107 90 nts SEQ ID NO: 620 Polypeptide encoded by SEQ ID NO: 619 30 aa SEQ ID NO: 621 HepC1a segment 108 90 nts SEQ ID NO: 622 Polypeptide encoded by SEQ ID NO: 621 30 aa SEQ ID NO: 623 HepC1a segment 109 90 nts SEQ ID NO: 624 Polypeptide encoded by SEQ ID NO: 623 30 aa SEQ ID NO: 625 HepC1a segment 110 90 nts SEQ ID NO: 626 Polypeptide encoded by SEQ ID NO: 625 30 aa SEQ ID NO: 627 HepC1a segment 111 90 nts SEQ ID NO: 628 Polypeptide encoded by SEQ ID NO: 627 30 aa SEQ ID NO: 629 HepC1a segment 112 90 nts SEQ ID NO: 630 Polypeptide encoded by SEQ ID NO: 629 30 aa SEQ ID NO: 631 HepC1a segment 113 90 nts SEQ ID NO: 632 Polypeptide encoded by SEQ ID NO: 631 30 aa SEQ ID NO: 633 HepC1a segment 114 90 nts SEQ ID NO: 634 Polypeptide encoded by SEQ ID NO: 633 30 aa SEQ ID NO: 635 HepC1a segment 115 90 nts SEQ ID NO: 636 Polypeptide encoded by SEQ ID NO: 635 30 aa SEQ ID NO: 637 HepC1a segment 116 90 nts SEQ ID NO: 638 Polypeptide encoded by SEQ ID NO: 637 30 aa SEQ ID NO: 639 HepC1a segment 117 90 nts SEQ ID NO: 640 Polypeptide encoded by SEQ ID NO: 639 30 aa SEQ ID NO: 641 HepC1a segment 118 90 nts SEQ ID NO: 642 Polypeptide encoded by SEQ ID NO: 641 30 aa SEQ ID NO: 643 HepC1a segment 119 90 nts SEQ ID NO: 644 Polypeptide encoded by SEQ ID NO: 643 30 aa SEQ ID NO: 645 HepC1a segment 120 90 nts SEQ ID NO: 646 Polypeptide encoded by SEQ ID NO: 645 30 aa SEQ ID NO: 647 HepC1a segment 121 90 nts SEQ ID NO: 648 Polypeptide encoded by SEQ ID NO: 647 30 aa SEQ ID NO: 649 HepC1a segment 122 90 nts SEQ ID NO: 650 Polypeptide encoded by SEQ ID NO: 649 30 aa SEQ ID NO: 651 HepC1a segment 123 90 nts SEQ ID NO: 652 Polypeptide encoded by SEQ ID NO: 651 30 aa SEQ ID NO: 653 HepC1a segment 124 90 nts SEQ ID NO: 654 Polypeptide encoded by SEQ ID NO: 653 30 aa SEQ ID NO: 655 HepC1a segment 125 90 nts SEQ ID NO: 656 Polypeptide encoded by SEQ ID NO: 655 30 aa SEQ ID NO: 657 HepC1a segment 126 90 nts SEQ ID NO: 658 Polypeptide encoded by SEQ ID NO: 657 30 aa SEQ ID NO: 659 HepC1a segment 127 90 nts SEQ ID NO: 660 Polypeptide encoded by SEQ ID NO: 659 30 aa SEQ ID NO: 661 HepC1a segment 128 90 nts SEQ ID NO: 662 Polypeptide encoded by SEQ ID NO: 661 30 aa SEQ ID NO: 663 HepC1a segment 129 90 nts SEQ ID NO: 664 Polypeptide encoded by SEQ ID NO: 663 30 aa SEQ ID NO: 665 HepC1a segment 130 90 nts SEQ ID NO: 666 Polypeptide encoded by SEQ ID NO: 665 30 aa SEQ ID NO: 667 HepC1a segment 131 90 nts SEQ ID NO: 668 Polypeptide encoded by SEQ ID NO: 667 30 aa SEQ ID NO: 669 HepC1a segment 132 90 nts SEQ ID NO: 670 Polypeptide encoded by SEQ ID NO: 669 30 aa SEQ ID NO: 671 HepC1a segment 133 90 nts SEQ ID NO: 672 Polypeptide encoded by SEQ ID NO: 671 30 aa SEQ ID NO: 673 HepC1a segment 134 90 nts SEQ ID NO: 674 Polypeptide encoded by SEQ ID NO: 673 30 aa SEQ ID NO: 675 HepC1a segment 135 90 nts SEQ ID NO: 676 Polypeptide encoded by SEQ ID NO: 675 30 aa SEQ ID NO: 677 HepC1a segment 136 90 nts SEQ ID NO: 678 Polypeptide encoded by SEQ ID NO: 677 30 aa SEQ ID NO: 679 HepC1a segment 137 90 nts SEQ ID NO: 680 Polypeptide encoded by SEQ ID NO: 679 30 aa SEQ ID NO: 681 HepC1a segment 138 90 nts SEQ ID NO: 682 Polypeptide encoded by SEQ ID NO: 681 30 aa SEQ ID NO: 683 HepC1a segment 139 90 nts SEQ ID NO: 684 Polypeptide encoded by SEQ ID NO: 683 30 aa SEQ ID NO: 685 HepC1a segment 140 90 nts SEQ ID NO: 686 Polypeptide encoded by SEQ ID NO: 685 30 aa SEQ ID NO: 687 HepC1a segment 141 90 nts SEQ ID NO: 688 Polypeptide encoded by SEQ ID NO: 687 30 aa SEQ ID NO: 689 HepC1a segment 142 90 nts SEQ ID NO: 690 Polypeptide encoded by SEQ ID NO: 689 30 aa SEQ ID NO: 691 HepC1a segment 143 90 nts SEQ ID NO: 692 Polypeptide encoded by SEQ ID NO: 691 30 aa SEQ ID NO: 693 HepC1a segment 144 90 nts SEQ ID NO: 694 Polypeptide encoded by SEQ ID NO: 693 30 aa SEQ ID NO: 695 HepC1a segment 145 90 nts SEQ ID NO: 696 Polypeptide encoded by SEQ ID NO: 695 30 aa SEQ ID NO: 697 HepC1a segment 146 90 nts SEQ ID NO: 698 Polypeptide encoded by SEQ ID NO: 697 30 aa SEQ ID NO: 699 HepC1a segment 147 90 nts SEQ ID NO: 700 Polypeptide encoded by SEQ ID NO: 699 30 aa SEQ ID NO: 701 HepC1a segment 148 90 nts SEQ ID NO: 702 Polypeptide encoded by SEQ ID NO: 701 30 aa SEQ ID NO: 703 HepC1a segment 149 90 nts SEQ ID NO: 704 Polypeptide encoded by SEQ ID NO: 703 30 aa SEQ ID NO: 705 HepC1a segment 150 90 nts SEQ ID NO: 706 Polypeptide encoded by SEQ ID NO: 705 30 aa SEQ ID NO: 707 HepC1a segment 151 90 nts SEQ ID NO: 708 Polypeptide encoded by SEQ ID NO: 707 30 aa SEQ ID NO: 709 HepC1a segment 152 90 nts SEQ ID NO: 710 Polypeptide encoded by SEQ ID NO: 709 30 aa SEQ ID NO: 711 HepC1a segment 153 90 nts SEQ ID NO: 712 Polypeptide encoded by SEQ ID NO: 711 30 aa SEQ ID NO: 713 HepC1a segment 154 90 nts SEQ ID NO: 714 Polypeptide encoded by SEQ ID NO: 713 30 aa SEQ ID NO: 715 HepC1a segment 155 90 nts SEQ ID NO: 716 Polypeptide encoded by SEQ ID NO: 715 30 aa SEQ ID NO: 717 HepC1a segment 156 90 nts SEQ ID NO: 718 Polypeptide encoded by SEQ ID NO: 717 30 aa SEQ ID NO: 719 HepC1a segment 157 90 nts SEQ ID NO: 720 Polypeptide encoded by SEQ ID NO: 719 30 aa SEQ ID NO: 721 HepC1a segment 158 90 nts SEQ ID NO: 722 Polypeptide encoded by SEQ ID NO: 721 30 aa SEQ ID NO: 723 HepC1a segment 159 90 nts SEQ ID NO: 724 Polypeptide encoded by SEQ ID NO: 723 30 aa SEQ ID NO: 725 HepC1a segment 160 90 nts SEQ ID NO: 726 Polypeptide encoded by SEQ ID NO: 725 30 aa SEQ ID NO: 727 HepC1a segment 161 90 nts SEQ ID NO: 728 Polypeptide encoded by SEQ ID NO: 727 30 aa SEQ ID NO: 729 HepC1a segment 162 90 nts SEQ ID NO: 730 Polypeptide encoded by SEQ ID NO: 729 30 aa SEQ ID NO: 731 HepC1a segment 163 90 nts SEQ ID NO: 732 Polypeptide encoded by SEQ ID NO: 731 30 aa SEQ ID NO: 733 HepC1a segment 164 90 nts SEQ ID NO: 734 Polypeptide encoded by SEQ ID NO: 733 30 aa SEQ ID NO: 735 HepC1a segment 165 90 nts SEQ ID NO: 736 Polypeptide encoded by SEQ ID NO: 735 30 aa SEQ ID NO: 737 HepC1a segment 166 90 nts SEQ ID NO: 738 Polypeptide encoded by SEQ ID NO: 737 30 aa SEQ ID NO: 739 HepC1a segment 167 90 nts SEQ ID NO: 740 Polypeptide encoded by SEQ ID NO: 739 30 aa SEQ ID NO: 741 HepC1a segment 168 90 nts SEQ ID NO: 742 Polypeptide encoded by SEQ ID NO: 741 30 aa SEQ ID NO: 743 HepC1a segment 169 90 nts SEQ ID NO: 744 Polypeptide encoded by SEQ ID NO: 743 30 aa SEQ ID NO: 745 HepC1a segment 170 90 nts SEQ ID NO: 746 Polypeptide encoded by SEQ ID NO: 745 30 aa SEQ ID NO: 747 HepC1a segment 171 90 nts SEQ ID NO: 748 Polypeptide encoded by SEQ ID NO: 747 30 aa SEQ ID NO: 749 HepC1a segment 172 90 nts SEQ ID NO: 750 Polypeptide encoded by SEQ ID NO: 749 30 aa SEQ ID NO: 751 HepC1a segment 173 90 nts SEQ ID NO: 752 Polypeptide encoded by SEQ ID NO: 751 30 aa SEQ ID NO: 753 HepC1a segment 174 90 nts SEQ ID NO: 754 Polypeptide encoded by SEQ ID NO: 753 30 aa SEQ ID NO: 755 HepC1a segment 175 90 nts SEQ ID NO: 756 Polypeptide encoded by SEQ ID NO: 755 30 aa SEQ ID NO: 757 HepC1a segment 176 90 nts SEQ ID NO: 758 Polypeptide encoded by SEQ ID NO: 757 30 aa SEQ ID NO: 759 HepC1a segment 177 90 nts SEQ ID NO: 760 Polypeptide encoded by SEQ ID NO: 759 30 aa SEQ ID NO: 761 HepC1a segment 178 90 nts SEQ ID NO: 762 Polypeptide encoded by SEQ ID NO: 761 30 aa SEQ ID NO: 763 HepC1a segment 179 90 nts SEQ ID NO: 764 Polypeptide encoded by SEQ ID NO: 763 30 aa SEQ ID NO: 765 HepC1a segment 180 90 nts SEQ ID NO: 766 Polypeptide encoded by SEQ ID NO: 765 30 aa SEQ ID NO: 767 HepC1a segment 181 90 nts SEQ ID NO: 768 Polypeptide encoded by SEQ ID NO: 767 30 aa SEQ ID NO: 769 HepC1a segment 182 90 nts SEQ ID NO: 770 Polypeptide encoded by SEQ ID NO: 769 30 aa SEQ ID NO: 771 HepC1a segment 183 90 nts SEQ ID NO: 772 Polypeptide encoded by SEQ ID NO: 771 30 aa SEQ ID NO: 773 HepC1a segment 184 90 nts SEQ ID NO: 774 Polypeptide encoded by SEQ ID NO: 773 30 aa SEQ ID NO: 775 HepC1a segment 185 90 nts SEQ ID NO: 776 Polypeptide encoded by SEQ ID NO: 775 30 aa SEQ ID NO: 777 HepC1a segment 186 90 nts SEQ ID NO: 778 Polypeptide encoded by SEQ ID NO: 777 30 aa SEQ ID NO: 779 HepC1a segment 187 90 nts SEQ ID NO: 780 Polypeptide encoded by SEQ ID NO: 779 30 aa SEQ ID NO: 781 HepC1a segment 188 90 nts SEQ ID NO: 782 Polypeptide encoded by SEQ ID NO: 781 30 aa SEQ ID NO: 783 HepC1a segment 189 90 nts SEQ ID NO: 784 Polypeptide encoded by SEQ ID NO: 783 30 aa SEQ ID NO: 785 HepC1a segment 190 90 nts SEQ ID NO: 786 Polypeptide encoded by SEQ ID NO: 785 30 aa SEQ ID NO: 787 HepC1a segment 191 90 nts SEQ ID NO: 788 Polypeptide encoded by SEQ ID NO: 787 30 aa SEQ ID NO: 789 HepC1a segment 192 90 nts SEQ ID NO: 790 Polypeptide encoded by SEQ ID NO: 789 30 aa SEQ ID NO: 791 HepC1a segment 193 90 nts SEQ ID NO: 792 Polypeptide encoded by SEQ ID NO: 791 30 aa SEQ ID NO: 793 HepC1a segment 194 90 nts SEQ ID NO: 794 Polypeptide encoded by SEQ ID NO: 793 30 aa SEQ ID NO: 795 HepC1a segment 195 90 nts SEQ ID NO: 796 Polypeptide encoded by SEQ ID NO: 795 30 aa SEQ ID NO: 797 HepC1a segment 196 90 nts SEQ ID NO: 798 Polypeptide encoded by SEQ ID NO: 797 30 aa SEQ ID NO: 799 HepC1a segment 197 90 nts SEQ ID NO: 800 Polypeptide encoded by SEQ ID NO: 799 30 aa SEQ ID NO: 801 HepC1a segment 198 90 nts SEQ ID NO: 802 Polypeptide encoded by SEQ ID NO: 801 30 aa SEQ ID NO: 803 HepC1a segment 199 90 nts SEQ ID NO: 804 Polypeptide encoded by SEQ ID NO: 803 30 aa SEQ ID NO: 805 HepC1a segment 200 90 nts SEQ ID NO: 806 Polypeptide encoded by SEQ ID NO: 805 30 aa SEQ ID NO: 807 HepC1a segment 201 45 nts SEQ ID NO: 808 Polypeptide encoded by SEQ ID NO: 807 15 aa SEQ ID NO: 809 HepC1a scrambled 17955 nts SEQ ID NO: 810 Polypeptide encoded by SEQ ID NO: 809 5985 aa SEQ ID NO: 811 HepC Cassette A 6065 nts SEQ ID NO: 812 Polypeptide encoded by SEQ ID NO: 811 2011 aa SEQ ID NO: 813 HepC Cassette B 6069 nts SEQ ID NO: 814 Polypeptide encoded by SEQ ID NO: 813 2010 aa SEQ ID NO: 815 HepC Cassette C 6030 nts SEQ ID NO: 816 Polypeptide encoded by SEQ ID NO: 815 1997 aa SEQ ID NO: 817 gp100 consensus polypeptide 661 aa SEQ ID NO: 818 MART consensus polypeptide 118 aa SEQ ID NO: 819 TRP-1 consensus polypeptide 248 aa SEQ ID NO: 820 Tyros consensus polypeptide 529 aa SEQ ID NO: 821 TRP2 consensus polypeptide 519 aa SEQ ID NO: 822 MC1R consensus polypeptide 317 aa SEQ ID NO: 823 MUC1F consensus polypeptide 125 aa SEQ ID NO: 824 MUC1R consensus polypeptide 312 aa SEQ ID NO: 825 BAGE consensus polypeptide 43 aa SEQ ID NO: 826 GAGE-1 consensus polypeptide 138 aa SEQ ID NO: 827 gp1001n4 consensus polypeptide 51 aa SEQ ID NO: 828 MAGE-1 consensus polypeptide 309 aa SEQ ID NO: 829 MAGE-3 consensus polypeptide 314 aa SEQ ID NO: 830 PRAME consensus polypeptide 509 aa SEQ ID NO: 831 TRP21N2 consensus polypeptide 54 aa SEQ ID NO: 832 NYNSO1a consensus polypeptide 180 aa SEQ ID NO: 833 NYNSO1b consensus polypeptide 58 aa SEQ ID NO: 834 LAGE1 consensus polypeptide 180 aa SEQ ID NO: 835 gp100 segment 1 90 nts SEQ ID NO: 836 Polypeptide encoded by SEQ ID NO: 835 30 aa SEQ ID NO: 837 gp100 segment 2 90 nts SEQ ID NO: 838 Polypeptide encoded by SEQ ID NO: 837 30 aa SEQ ID NO: 839 gp100 segment 3 90 nts SEQ ID NO: 840 Polypeptide encoded by SEQ ID NO: 839 30 aa SEQ ID NO: 841 gp100 segment 4 90 nts SEQ ID NO: 842 Polypeptide encoded by SEQ ID NO: 841 30 aa SEQ ID NO: 843 gp100 segment 5 90 nts SEQ ID NO: 844 Polypeptide encoded by SEQ ID NO: 843 30 aa SEQ ID NO: 845 gp100 segment 6 90 nts SEQ ID NO: 846 Polypeptide encoded by SEQ ID NO: 845 30 aa SEQ ID NO: 847 gp100 segment 7 90 nts SEQ ID NO: 848 Polypeptide encoded by SEQ ID NO: 847 30 aa SEQ ID NO: 849 gp100 segment 8 90 nts SEQ ID NO: 850 Polypeptide encoded by SEQ ID NO: 849 30 aa SEQ ID NO: 851 gp100 segment 9 90 nts SEQ ID NO: 852 Polypeptide encoded by SEQ ID NO: 851 30 aa SEQ ID NO: 853 gp100 segment 10 90 nts SEQ ID NO: 854 Polypeptide encoded by SEQ ID NO: 853 30 aa SEQ ID NO: 855 gp100 segment 11 90 nts SEQ ID NO: 856 Polypeptide encoded by SEQ ID NO: 855 30 aa SEQ ID NO: 857 gp100 segment 12 90 nts SEQ ID NO: 858 Polypeptide encoded by SEQ ID NO: 857 30 aa SEQ ID NO: 859 gp100 segment 13 90 nts SEQ ID NO: 860 Polypeptide encoded by SEQ ID NO: 859 30 aa SEQ ID NO: 861 gp100 segment 14 90 nts SEQ ID NO: 862 Polypeptide encoded by SEQ ID NO: 861 30 aa SEQ ID NO: 863 gp100 segment 15 90 nts SEQ ID NO: 864 Polypeptide encoded by SEQ ID NO: 863 30 aa SEQ ID NO: 865 gp100 segment 16 90 nts SEQ ID NO: 866 Polypeptide encoded by SEQ ID NO: 865 30 aa SEQ ID NO: 867 gp100 segment 17 90 nts SEQ ID NO: 868 Polypeptide encoded by SEQ ID NO: 867 30 aa SEQ ID NO: 869 gp100 segment 18 90 nts SEQ ID NO: 870 Polypeptide encoded by SEQ ID NO: 869 30 aa SEQ ID NO: 871 gp100 segment 19 90 nts SEQ ID NO: 872 Polypeptide encoded by SEQ ID NO: 871 30 aa SEQ ID NO: 873 gp100 segment 20 90 nts SEQ ID NO: 874 Polypeptide encoded by SEQ ID NO: 873 30 aa SEQ ID NO: 875 gp100 segment 21 90 nts SEQ ID NO: 876 Polypeptide encoded by SEQ ID NO: 875 30 aa SEQ ID NO: 877 gp100 segment 22 90 nts SEQ ID NO: 878 Polypeptide encoded by SEQ ID NO: 877 30 aa SEQ ID NO: 879 gp100 segment 23 90 nts SEQ ID NO: 880 Polypeptide encoded by SEQ ID NO: 879 30 aa SEQ ID NO: 881 gp100 segment 24 90 nts SEQ ID NO: 882 Polypeptide encoded by SEQ ID NO: 881 30 aa SEQ ID NO: 883 gp100 segment 25 90 nts SEQ ID NO: 884 Polypeptide encoded by SEQ ID NO: 883 30 aa SEQ ID NO: 885 gp100 segment 26 90 nts SEQ ID NO: 886 Polypeptide encoded by SEQ ID NO: 885 30 aa SEQ ID NO: 887 gp100 segment 27 90 nts SEQ ID NO: 888 Polypeptide encoded by SEQ ID NO: 887 30 aa SEQ ID NO: 889 gp100 segment 28 90 nts SEQ ID NO: 890 Polypeptide encoded by SEQ ID NO: 889 30 aa SEQ ID NO: 891 gp100 segment 29 90 nts SEQ ID NO: 892 Polypeptide encoded by SEQ ID NO: 891 30 aa SEQ ID NO: 893 gp100 segment 30 90 nts SEQ ID NO: 894 Polypeptide encoded by SEQ ID NO: 893 30 aa SEQ ID NO: 895 gp100 segment 31 90 nts SEQ ID NO: 896 Polypeptide encoded by SEQ ID NO: 895 30 aa SEQ ID NO: 897 gp100 segment 32 90 nts SEQ ID NO: 898 Polypeptide encoded by SEQ ID NO: 897 30 aa SEQ ID NO: 899 gp100 segment 33 90 nts SEQ ID NO: 900 Polypeptide encoded by SEQ ID NO: 899 30 aa SEQ ID NO: 901 gp100 segment 34 90 nts SEQ ID NO: 902 Polypeptide encoded by SEQ ID NO: 901 30 aa SEQ ID NO: 903 gp100 segment 35 90 nts SEQ ID NO: 904 Polypeptide encoded by SEQ ID NO: 903 30 aa SEQ ID NO: 905 gp100 segment 36 90 nts SEQ ID NO: 906 Polypeptide encoded by SEQ ID NO: 905 30 aa SEQ ID NO: 907 gp100 segment 37 90 nts SEQ ID NO: 908 Polypeptide encoded by SEQ ID NO: 907 30 aa SEQ ID NO: 909 gp100 segment 38 90 nts SEQ ID NO: 910 Polypeptide encoded by SEQ ID NO: 909 30 aa SEQ ID NO: 911 gp100 segment 39 90 nts SEQ ID NO: 912 Polypeptide encoded by SEQ ID NO: 911 30 aa SEQ ID NO: 913 gp100 segment 40 90 nts SEQ ID NO: 914 Polypeptide encoded by SEQ ID NO: 913 30 aa SEQ ID NO: 915 gp100 segment 41 90 nts SEQ ID NO: 916 Polypeptide encoded by SEQ ID NO: 915 30 aa SEQ ID NO: 917 gp100 segment 42 90 nts SEQ ID NO: 918 Polypeptide encoded by SEQ ID NO: 917 30 aa SEQ ID NO: 919 gp100 segment 43 90 nts SEQ ID NO: 920 Polypeptide encoded by SEQ ID NO: 919 30 aa SEQ ID NO: 921 gp100 segment 44 60 nts SEQ ID NO: 922 Polypeptide encoded by SEQ ID NO: 921 20 aa SEQ ID NO: 923 MART segment 1 90 nts SEQ ID NO: 924 Polypeptide encoded by SEQ ID NO: 923 30 aa SEQ ID NO: 925 MART segment 2 90 nts SEQ ID NO: 926 Polypeptide encoded by SEQ ID NO: 925 30 aa SEQ ID NO: 927 MART segment 3 90 nts SEQ ID NO: 928 Polypeptide encoded by SEQ ID NO: 927 30 aa SEQ ID NO: 929 MART segment 4 90 nts SEQ ID NO: 930 Polypeptide encoded by SEQ ID NO: 929 30 aa SEQ ID NO: 931 MART segment 5 90 nts SEQ ID NO: 932 Polypeptide encoded by SEQ ID NO: 931 30 aa SEQ ID NO: 933 MART segment 6 90 nts SEQ ID NO: 934 Polypeptide encoded by SEQ ID NO: 933 30 aa SEQ ID NO: 935 MART segment 7 90 nts SEQ ID NO: 936 Polypeptide encoded by SEQ ID NO: 935 30 aa SEQ ID NO: 937 MART segment 8 51 nts SEQ ID NO: 938 Polypeptide encoded by SEQ ID NO: 937 17 aa SEQ ID NO: 939 trp-1 segment 1 90 nts SEQ ID NO: 940 Polypeptide encoded by SEQ ID NO: 939 30 aa SEQ ID NO: 941 trp-1 segment 2 90 nts SEQ ID NO: 942 Polypeptide encoded by SEQ ID NO: 941 30 aa SEQ ID NO: 943 trp-1 segment 3 90 nts SEQ ID NO: 944 Polypeptide encoded by SEQ ID NO: 943 30 aa SEQ ID NO: 945 trp-1 segment 4 90 nts SEQ ID NO: 946 Polypeptide encoded by SEQ ID NO: 945 30 aa SEQ ID NO: 947 trp-1 segment 5 90 nts SEQ ID NO: 948 Polypeptide encoded by SEQ ID NO: 947 30 aa SEQ ID NO: 949 trp-1 segment 6 90 nts SEQ ID NO: 950 Polypeptide encoded by SEQ ID NO: 949 30 aa SEQ ID NO: 951 trp-1 segment 7 90 nts SEQ ID NO: 952 Polypeptide encoded by SEQ ID NO: 951 30 aa SEQ ID NO: 953 trp-1 segment 8 90 nts SEQ ID NO: 954 Polypeptide encoded by SEQ ID NO: 953 30 aa SEQ ID NO: 955 trp-1 segment 9 90 nts SEQ ID NO: 956 Polypeptide encoded by SEQ ID NO: 955 30 aa SEQ ID NO: 957 trp-1 segment 10 90 nts SEQ ID NO: 958 Polypeptide encoded by SEQ ID NO: 957 30 aa SEQ ID NO: 959 trp-1 segment 11 90 nts SEQ ID NO: 960 Polypeptide encoded by SEQ ID NO: 959 30 aa SEQ ID NO: 961 trp-1 segment 12 90 nts SEQ ID NO: 962 Polypeptide encoded by SEQ ID NO: 961 30 aa SEQ ID NO: 963 trp-1 segment 13 90 nts SEQ ID NO: 964 Polypeptide encoded by SEQ ID NO: 963 30 aa SEQ ID NO: 965 trp-1 segment 14 90 nts SEQ ID NO: 966 Polypeptide encoded by SEQ ID NO: 965 30 aa SEQ ID NO: 967 trp-1 segment 15 90 nts SEQ ID NO: 968 Polypeptide encoded by SEQ ID NO: 967 30 aa SEQ ID NO: 969 trp-1 segment 16 81 nts SEQ ID NO: 970 Polypeptide encoded by SEQ ID NO: 969 27 aa SEQ ID NO: 971 tyros segment 1 90 nts SEQ ID NO: 972 Polypeptide encoded by SEQ ID NO: 971 30 aa SEQ ID NO: 973 tyros segment 2 90 nts SEQ ID NO: 974 Polypeptide encoded by SEQ ID NO: 973 30 aa SEQ ID NO: 975 tyros segment 3 90 nts SEQ ID NO: 976 Polypeptide encoded by SEQ ID NO: 975 30 aa SEQ ID NO: 977 tyros segment 4 90 nts SEQ ID NO: 978 Polypeptide encoded by SEQ ID NO: 977 30 aa SEQ ID NO: 979 tyros segment 5 90 nts SEQ ID NO: 980 Polypeptide encoded by SEQ ID NO: 979 30 aa SEQ ID NO: 981 tyros segment 6 90 nts SEQ ID NO: 982 Polypeptide encoded by SEQ ID NO: 981 30 aa SEQ ID NO: 983 tyros segment 7 90 nts SEQ ID NO: 984 Polypeptide encoded by SEQ ID NO: 983 30 aa SEQ ID NO: 985 tyros segment 8 90 nts SEQ ID NO: 986 Polypeptide encoded by SEQ ID NO: 985 30 aa SEQ ID NO: 987 tyros segment 9 90 nts SEQ ID NO: 988 Polypeptide encoded by SEQ ID NO: 987 30 aa SEQ ID NO: 989 tyros segment 10 90 nts SEQ ID NO: 990 Polypeptide encoded by SEQ ID NO: 989 30 aa SEQ ID NO: 991 tyros segment 11 90 nts SEQ ID NO: 992 Polypeptide encoded by SEQ ID NO: 991 30 aa SEQ ID NO: 993 tyros segment 12 90 nts SEQ ID NO: 994 Polypeptide encoded by SEQ ID NO: 993 30 aa SEQ ID NO: 995 tyros segment 13 90 nts SEQ ID NO: 996 Polypeptide encoded by SEQ ID NO: 995 30 aa SEQ ID NO: 997 tyros segment 14 90 nts SEQ ID NO: 998 Polypeptide encoded by SEQ ID NO: 997 30 aa SEQ ID NO: 999 tyros segment 15 90 nts SEQ ID NO: 1000 Polypeptide encoded by SEQ ID NO: 999 30 aa SEQ ID NO: 1001 tyros segment 16 90 nts SEQ ID NO: 1002 Polypeptide encoded by SEQ ID NO: 1001 30 aa SEQ ID NO: 1003 tyros segment 17 90 nts SEQ ID NO: 1004 Polypeptide encoded by SEQ ID NO: 1003 30 aa SEQ ID NO: 1005 tyros segment 18 90 nts SEQ ID NO: 1006 Polypeptide encoded by SEQ ID NO: 1005 30 aa SEQ ID NO: 1007 tyros segment 19 90 nts SEQ ID NO: 1008 Polypeptide encoded by SEQ ID NO: 1007 30 aa SEQ ID NO: 1009 tyros segment 20 90 nts SEQ ID NO: 1010 Polypeptide encoded by SEQ ID NO: 1009 30 aa SEQ ID NO: 1011 tyros segment 21 90 nts SEQ ID NO: 1012 Polypeptide encoded by SEQ ID NO: 1011 30 aa SEQ ID NO: 1013 tyros segment 22 90 nts SEQ ID NO: 1014 Polypeptide encoded by SEQ ID NO: 1013 30 aa SEQ ID NO: 1015 tyros segment 23 90 nts SEQ ID NO: 1016 Polypeptide encoded by SEQ ID NO: 1015 30 aa SEQ ID NO: 1017 tyros segment 24 90 nts SEQ ID NO: 1018 Polypeptide encoded by SEQ ID NO: 1017 30 aa SEQ ID NO: 1019 tyros segment 25 90 nts SEQ ID NO: 1020 Polypeptide encoded by SEQ ID NO: 1019 30 aa SEQ ID NO: 1021 tyros segment 26 90 nts SEQ ID NO: 1022 Polypeptide encoded by SEQ ID NO: 1021 30 aa SEQ ID NO: 1023 tyros segment 27 90 nts SEQ ID NO: 1024 Polypeptide encoded by SEQ ID NO: 1023 30 aa SEQ ID NO: 1025 tyros segment 28 90 nts SEQ ID NO: 1026 Polypeptide encoded by SEQ ID NO: 1025 30 aa SEQ ID NO: 1027 tyros segment 29 90 nts SEQ ID NO: 1028 Polypeptide encoded by SEQ ID NO: 1027 30 aa SEQ ID NO: 1029 tyros segment 30 90 nts SEQ ID NO: 1030 Polypeptide encoded by SEQ ID NO: 1029 30 aa SEQ ID NO: 1031 tyros segment 31 90 nts SEQ ID NO: 1032 Polypeptide encoded by SEQ ID NO: 1031 30 aa SEQ ID NO: 1033 tyros segment 32 90 nts SEQ ID NO: 1034 Polypeptide encoded by SEQ ID NO: 1033 30 aa SEQ ID NO: 1035 tyros segment 33 90 nts SEQ ID NO: 1036 Polypeptide encoded by SEQ ID NO: 1035 30 aa SEQ ID NO: 1037 tyros segment 34 90 nts SEQ ID NO: 1038 Polypeptide encoded by SEQ ID NO: 1037 30 aa SEQ ID NO: 1039 tyros segment 35 69 nts SEQ ID NO: 1040 Polypeptide encoded by SEQ ID NO: 1039 23 aa SEQ ID NO: 1041 trp2 segment 1 90 nts SEQ ID NO: 1042 Polypeptide encoded by SEQ ID NO: 1041 30 aa SEQ ID NO: 1043 trp2 segment 2 90 nts SEQ ID NO: 1044 Polypeptide encoded by SEQ ID NO: 1043 30 aa SEQ ID NO: 1045 trp2 segment 3 90 nts SEQ ID NO: 1046 Polypeptide encoded by SEQ ID NO: 1045 30 aa SEQ ID NO: 1047 trp2 segment 4 90 nts SEQ ID NO: 1048 Polypeptide encoded by SEQ ID NO: 1047 30 aa SEQ ID NO: 1049 trp2 segment 5 90 nts SEQ ID NO: 1050 Polypeptide encoded by SEQ ID NO: 1049 30 aa SEQ ID NO: 1051 trp2 segment 6 90 nts SEQ ID NO: 1052 Polypeptide encoded by SEQ ID NO: 1051 30 aa SEQ ID NO: 1053 trp2 segment 7 90 nts SEQ ID NO: 1054 Polypeptide encoded by SEQ ID NO: 1053 30 aa SEQ ID NO: 1055 trp2 segment 8 90 nts SEQ ID NO: 1056 Polypeptide encoded by SEQ ID NO: 1055 30 aa SEQ ID NO: 1057 trp2 segment 9 90 nts SEQ ID NO: 1058 Polypeptide encoded by SEQ ID NO: 1057 30 aa SEQ ID NO: 1059 trp2 segment 10 90 nts SEQ ID NO: 1060 Polypeptide encoded by SEQ ID NO: 1059 30 aa SEQ ID NO: 1061 trp2 segment 11 90 nts SEQ ID NO: 1062 Polypeptide encoded by SEQ ID NO: 1061 30 aa SEQ ID NO: 1063 trp2 segment 12 90 nts SEQ ID NO: 1064 Polypeptide encoded by SEQ ID NO: 1063 30 aa SEQ ID NO: 1065 trp2 segment 13 90 nts SEQ ID NO: 1066 Polypeptide encoded by SEQ ID NO: 1065 30 aa SEQ ID NO: 1067 trp2 segment 14 90 nts SEQ ID NO: 1068 Polypeptide encoded by SEQ ID NO: 1067 30 aa SEQ ID NO: 1069 trp2 segment 15 90 nts SEQ ID NO: 1070 Polypeptide encoded by SEQ ID NO: 1069 30 aa SEQ ID NO: 1071 trp2 segment 16 90 nts SEQ ID NO: 1072 Polypeptide encoded by SEQ ID NO: 1071 30 aa SEQ ID NO: 1073 trp2 segment 17 90 nts SEQ ID NO: 1074 Polypeptide encoded by SEQ ID NO: 1073 30 aa SEQ ID NO: 1075 trp2 segment 18 90 nts SEQ ID NO: 1076 Polypeptide encoded by SEQ ID NO: 1075 30 aa SEQ ID NO: 1077 trp2 segment 19 90 nts SEQ ID NO: 1078 Polypeptide encoded by SEQ ID NO: 1077 30 aa SEQ ID NO: 1079 trp2 segment 20 90 nts SEQ ID NO: 1080 Polypeptide encoded by SEQ ID NO: 1079 30 aa SEQ ID NO: 1081 trp2 segment 21 90 nts SEQ ID NO: 1082 Polypeptide encoded by SEQ ID NO: 1081 30 aa SEQ ID NO: 1083 trp2 segment 22 90 nts SEQ ID NO: 1084 Polypeptide encoded by SEQ ID NO: 1083 30 aa SEQ ID NO: 1085 trp2 segment 23 90 nts SEQ ID NO: 1086 Polypeptide encoded by SEQ ID NO: 1085 30 aa SEQ ID NO: 1087 trp2 segment 24 90 nts SEQ ID NO: 1088 Polypeptide encoded by SEQ ID NO: 1087 30 aa SEQ ID NO: 1089 trp2 segment 25 90 nts SEQ ID NO: 1090 Polypeptide encoded by SEQ ID NO: 1089 30 aa SEQ ID NO: 1091 trp2 segment 26 90 nts SEQ ID NO: 1092 Polypeptide encoded by SEQ ID NO: 1091 30 aa SEQ ID NO: 1093 trp2 segment 27 90 nts SEQ ID NO: 1094 Polypeptide encoded by SEQ ID NO: 1093 30 aa SEQ ID NO: 1095 trp2 segment 28 90 nts SEQ ID NO: 1096 Polypeptide encoded by SEQ ID NO: 1095 30 aa SEQ ID NO: 1097 trp2 segment 29 90 nts SEQ ID NO: 1098 Polypeptide encoded by SEQ ID NO: 1097 30 aa SEQ ID NO: 1099 trp2 segment 30 90 nts SEQ ID NO: 1100 Polypeptide encoded by SEQ ID NO: 1099 30 aa SEQ ID NO: 1101 trp2 segment 31 90 nts SEQ ID NO: 1102 Polypeptide encoded by SEQ ID NO: 1101 30 aa SEQ ID NO: 1103 trp2 segment 32 90 nts SEQ ID NO: 1104 Polypeptide encoded by SEQ ID NO: 1103 30 aa SEQ ID NO: 1105 trp2 segment 33 90 nts SEQ ID NO: 1106 Polypeptide encoded by SEQ ID NO: 1105 30 aa SEQ ID NO: 1107 trp2 segment 34 84 nts SEQ ID NO: 1108 Polypeptide encoded by SEQ ID NO: 1107 28 aa SEQ ID NO: 1109 MC1R segment 1 90 nts SEQ ID NO: 1110 Polypeptide encoded by SEQ ID NO: 1109 30 aa SEQ ID NO: 1111 MC1R segment 2 90 nts SEQ ID NO: 1112 Polypeptide encoded by SEQ ID NO: 1111 30 aa SEQ ID NO: 1113 MC1R segment 3 90 nts SEQ ID NO: 1114 Polypeptide encoded by SEQ ID NO: 1113 30 aa SEQ ID NO: 1115 MC1R segment 4 90 nts SEQ ID NO: 1116 Polypeptide encoded by SEQ ID NO: 1115 30 aa SEQ ID NO: 1117 MC1R segment 5 90 nts SEQ ID NO: 1118 Polypeptide encoded by SEQ ID NO: 1117 30 aa SEQ ID NO: 1119 MC1R segment 6 90 nts SEQ ID NO: 1120 Polypeptide encoded by SEQ ID NO: 1119 30 aa SEQ ID NO: 1121 MC1R segment 7 90 nts SEQ ID NO: 1122 Polypeptide encoded by SEQ ID NO: 1121 30 aa SEQ ID NO: 1123 MC1R segment 8 90 nts SEQ ID NO: 1124 Polypeptide encoded by SEQ ID NO: 1123 30 aa SEQ ID NO: 1125 MC1R segment 9 90 nts SEQ ID NO: 1126 Polypeptide encoded by SEQ ID NO: 1125 30 aa SEQ ID NO: 1127 MC1R segment 10 90 nts SEQ ID NO: 1128 Polypeptide encoded by SEQ ID NO: 1127 30 aa SEQ ID NO: 1129 MC1R segment 11 90 nts SEQ ID NO: 1130 Polypeptide encoded by SEQ ID NO: 1129 30 aa SEQ ID NO: 1131 MC1R segment 12 90 nts SEQ ID NO: 1132 Polypeptide encoded by SEQ ID NO: 1131 30 aa SEQ ID NO: 1133 MC1R segment 13 90 nts SEQ ID NO: 1134 Polypeptide encoded by SEQ ID NO: 1133 30 aa SEQ ID NO: 1135 MC1R segment 14 90 nts SEQ ID NO: 1136 Polypeptide encoded by SEQ ID NO: 1135 30 aa SEQ ID NO: 1137 MC1R segment 15 90 nts SEQ ID NO: 1138 Polypeptide encoded by SEQ ID NO: 1137 30 aa SEQ ID NO: 1139 MC1R segment 16 90 nts SEQ ID NO: 1140 Polypeptide encoded by SEQ ID NO: 1139 30 aa SEQ ID NO: 1141 MC1R segment 17 90 nts SEQ ID NO: 1142 Polypeptide encoded by SEQ ID NO: 1141 30 aa SEQ ID NO: 1143 MC1R segment 18 90 nts SEQ ID NO: 1144 Polypeptide encoded by SEQ ID NO: 1143 30 aa SEQ ID NO: 1145 MC1R segment 19 90 nts SEQ ID NO: 1146 Polypeptide encoded by SEQ ID NO: 1145 30 aa SEQ ID NO: 1147 MC1R segment 20 90 nts SEQ ID NO: 1148 Polypeptide encoded by SEQ ID NO: 1147 30 aa SEQ ID NO: 1149 MC1R segment 21 63 nts SEQ ID NO: 1150 Polypeptide encoded by SEQ ID NO: 1149 21 aa SEQ ID NO: 1151 MUC1F segment 1 90 nts SEQ ID NO: 1152 Polypeptide encoded by SEQ ID NO: 1151 30 aa SEQ ID NO: 1153 MUC1F segment 2 90 nts SEQ ID NO: 1154 Polypeptide encoded by SEQ ID NO: 1153 30 aa SEQ ID NO: 1155 MUC1F segment 3 90 nts SEQ ID NO: 1156 Polypeptide encoded by SEQ ID NO: 1155 30 aa SEQ ID NO: 1157 MUC1F segment 4 90 nts SEQ ID NO: 1158 Polypeptide encoded by SEQ ID NO: 1157 30 aa SEQ ID NO: 1159 MUC1F segment 5 90 nts SEQ ID NO: 1160 Polypeptide encoded by SEQ ID NO: 1159 30 aa SEQ ID NO: 1161 MUC1F segment 6 90 nts SEQ ID NO: 1162 Polypeptide encoded by SEQ ID NO: 1161 30 aa SEQ ID NO: 1163 MUC1F segment 7 90 nts SEQ ID NO: 1164 Polypeptide encoded by SEQ ID NO: 1163 30 aa SEQ ID NO: 1165 MUC1F segment 8 72 nts SEQ ID NO: 1166 Polypeptide encoded by SEQ ID NO: 1165 24 aa SEQ ID NO: 1167 MUC1R segment 1 90 nts SEQ ID NO: 1168 Polypeptide encoded by SEQ ID NO: 1167 30 aa SEQ ID NO: 1169 MUC1R segment 2 90 nts SEQ ID NO: 1170 Polypeptide encoded by SEQ ID NO: 1169 30 aa SEQ ID NO: 1171 MUC1R segment 3 90 nts SEQ ID NO: 1172 Polypeptide encoded by SEQ ID NO: 1171 30 aa SEQ ID NO: 1173 MUC1R segment 4 90 nts SEQ ID NO: 1174 Polypeptide encoded by SEQ ID NO: 1173 30 aa SEQ ID NO: 1175 MUC1R segment 5 90 nts SEQ ID NO: 1176 Polypeptide encoded by SEQ ID NO: 1175 30 aa SEQ ID NO: 1177 MUC1R segment 6 90 nts SEQ ID NO: 1178 Polypeptide encoded by SEQ ID NO: 1177 30 aa SEQ ID NO: 1179 MUC1R segment 7 90 nts SEQ ID NO: 1180 Polypeptide encoded by SEQ ID NO: 1179 30 aa SEQ ID NO: 1181 MUC1R segment 8 90 nts SEQ ID NO: 1182 Polypeptide encoded by SEQ ID NO: 1181 30 aa SEQ ID NO: 1183 MUC1R segment 9 90 nts SEQ ID NO: 1184 Polypeptide encoded by SEQ ID NO: 1183 30 aa SEQ ID NO: 1185 MUC1R segment 10 90 nts SEQ ID NO: 1186 Polypeptide encoded by SEQ ID NO: 1185 30 aa SEQ ID NO: 1187 MUC1R segment 11 90 nts SEQ ID NO: 1188 Polypeptide encoded by SEQ ID NO: 1187 30 aa SEQ ID NO: 1189 MUC1R segment 12 90 nts SEQ ID NO: 1190 Polypeptide encoded by SEQ ID NO: 1189 30 aa SEQ ID NO: 1191 MUC1R segment 13 90 nts SEQ ID NO: 1192 Polypeptide encoded by SEQ ID NO: 1191 30 aa SEQ ID NO: 1193 MUC1R segment 14 90 nts SEQ ID NO: 1194 Polypeptide encoded by SEQ ID NO: 1193 30 aa SEQ ID NO: 1195 MUC1R segment 15 90 nts SEQ ID NO: 1196 Polypeptide encoded by SEQ ID NO: 1195 30 aa SEQ ID NO: 1197 MUC1R segment 16 90 nts SEQ ID NO: 1198 Polypeptide encoded by SEQ ID NO: 1197 30 aa SEQ ID NO: 1199 MUC1R segment 17 90 nts SEQ ID NO: 1200 Polypeptide encoded by SEQ ID NO: 1199 30 aa SEQ ID NO: 1201 MUC1R segment 18 90 nts SEQ ID NO: 1202 Polypeptide encoded by SEQ ID NO: 1201 30 aa SEQ ID NO: 1203 MUC1R segment 19 90 nts SEQ ID NO: 1204 Polypeptide encoded by SEQ ID NO: 1203 30 aa SEQ ID NO: 1205 MUC1R segment 20 90 nts SEQ ID NO: 1206 Polypeptide encoded by SEQ ID NO: 1205 30 aa SEQ ID NO: 1207 MUC1R segment 21 48 nts SEQ ID NO: 1208 Polypeptide encoded by SEQ ID NO: 1207 16 aa SEQ ID NO: 1209 Differentiation Savine 16638 nts SEQ ID NO: 1210 Polypeptide encoded by SEQ ID NO: 1209 5546 aa SEQ ID NO: 1211 BAGE segment 1 90 nts SEQ ID NO: 1212 Polypeptide encoded by SEQ ID NO: 1211 30 aa SEQ ID NO: 1213 BAGE segment 2 90 nts SEQ ID NO: 1214 Polypeptide encoded by SEQ ID NO: 1213 30 aa SEQ ID NO: 1215 BAGE segment 3 51 nts SEQ ID NO: 1216 Polypeptide encoded by SEQ ID NO: 1215 17 aa SEQ ID NO: 1217 GAGE-1 segment 1 90 nts SEQ ID NO: 1218 Polypeptide encoded by SEQ ID NO: 1217 30 aa SEQ ID NO: 1219 GAGE-1 segment 2 90 nts SEQ ID NO: 1220 Polypeptide encoded by SEQ ID NO: 1219 30 aa SEQ ID NO: 1221 GAGE-1 segment 3 90 nts SEQ ID NO: 1222 Polypeptide encoded by SEQ ID NO: 1221 30 aa SEQ ID NO: 1223 GAGE-1 segment 4 90 nts SEQ ID NO: 1224 Polypeptide encoded by SEQ ID NO: 1223 30 aa SEQ ID NO: 1225 GAGE-1 segment 5 90 nts SEQ ID NO: 1226 Polypeptide encoded by SEQ ID NO: 1225 30 aa SEQ ID NO: 1227 GAGE-1 segment 6 90 nts SEQ ID NO: 1228 Polypeptide encoded by SEQ ID NO: 1227 30 aa SEQ ID NO: 1229 GAGE-1 segment 7 90 nts SEQ ID NO: 1230 Polypeptide encoded by SEQ ID NO: 1229 30 aa SEQ ID NO: 1231 GAGE-1 segment 8 90 nts SEQ ID NO: 1232 Polypeptide encoded by SEQ ID NO: 1231 30 aa SEQ ID NO: 1233 GAGE-1 segment 9 66 nts SEQ ID NO: 1234 Polypeptide encoded by SEQ ID NO: 1233 22 aa SEQ ID NO: 1235 gp1001n4 segment 1 90 nts SEQ ID NO: 1236 Polypeptide encoded by SEQ ID NO: 1235 30 aa SEQ ID NO: 1237 gp1001n4 segment 2 90 nts SEQ ID NO: 1238 Polypeptide encoded by SEQ ID NO: 1237 30 aa SEQ ID NO: 1239 gp1001n4 segment 3 75 nts SEQ ID NO: 1240 Polypeptide encoded by SEQ ID NO: 1239 25 aa SEQ ID NO: 1241 MAGE-1 segment 1 90 nts SEQ ID NO: 1242 Polypeptide encoded by SEQ ID NO: 1241 30 aa SEQ ID NO: 1243 MAGE-1 segment 2 90 nts SEQ ID NO: 1244 Polypeptide encoded by SEQ ID NO: 1243 30 aa SEQ ID NO: 1245 MAGE-1 segment 3 90 nts SEQ ID NO: 1246 Polypeptide encoded by SEQ ID NO: 1245 30 aa SEQ ID NO: 1247 MAGE-1 segment 4 90 nts SEQ ID NO: 1248 Polypeptide encoded by SEQ ID NO: 1247 30 aa SEQ ID NO: 1249 MAGE-1 segment 5 90 nts SEQ ID NO: 1250 Polypeptide encoded by SEQ ID NO: 1249 30 aa SEQ ID NO: 1251 MAGE-1 segment 6 90 nts SEQ ID NO: 1252 Polypeptide encoded by SEQ ID NO: 1251 30 aa SEQ ID NO: 1253 MAGE-1 segment 7 90 nts SEQ ID NO: 1254 Polypeptide encoded by SEQ ID NO: 1253 30 aa SEQ ID NO: 1255 MAGE-1 segment 8 90 nts SEQ ID NO: 1256 Polypeptide encoded by SEQ ID NO: 1255 30 aa SEQ ID NO: 1257 MAGE-1 segment 9 90 nts SEQ ID NO: 1258 Polypeptide encoded by SEQ ID NO: 1257 30 aa SEQ ID NO: 1259 MAGE-1 segment 10 90 nts SEQ ID NO: 1260 Polypeptide encoded by SEQ ID NO: 1259 30 aa SEQ ID NO: 1261 MAGE-1 segment 11 90 nts SEQ ID NO: 1262 Polypeptide encoded by SEQ ID NO: 1261 30 aa SEQ ID NO: 1263 MAGE-1 segment 12 90 nts SEQ ID NO: 1264 Polypeptide encoded by SEQ ID NO: 1263 30 aa SEQ ID NO: 1265 MAGE-1 segment 13 90 nts SEQ ID NO: 1266 Polypeptide encoded by SEQ ID NO: 1265 30 aa SEQ ID NO: 1267 MAGE-1 segment 14 90 nts SEQ ID NO: 1268 Polypeptide encoded by SEQ ID NO: 1267 30 aa SEQ ID NO: 1269 MAGE-1 segment 15 90 nts SEQ ID NO: 1270 Polypeptide encoded by SEQ ID NO: 1269 30 aa SEQ ID NO: 1271 MAGE-1 segment 16 90 nts SEQ ID NO: 1272 Polypeptide encoded by SEQ ID NO: 1271 30 aa SEQ ID NO: 1273 MAGE-1 segment 17 90 nts SEQ ID NO: 1274 Polypeptide encoded by SEQ ID NO: 1273 30 aa SEQ ID NO: 1275 MAGE-1 segment 18 90 nts SEQ ID NO: 1276 Polypeptide encoded by SEQ ID NO: 1275 30 aa SEQ ID NO: 1277 MAGE-1 segment 19 90 nts SEQ ID NO: 1278 Polypeptide encoded by SEQ ID NO: 1277 30 aa SEQ ID NO: 1279 MAGE-1 segment 20 84 nts SEQ ID NO: 1280 Polypeptide encoded by SEQ ID NO: 1279 28 aa SEQ ID NO: 1281 MAGE-3 segment 1 90 nts SEQ ID NO: 1282 Polypeptide encoded by SEQ ID NO: 1281 30 aa SEQ ID NO: 1283 MAGE-3 segment 2 90 nts SEQ ID NO: 1284 Polypeptide encoded by SEQ ID NO: 1283 30 aa SEQ ID NO: 1285 MAGE-3 segment 3 90 nts SEQ ID NO: 1286 Polypeptide encoded by SEQ ID NO: 1285 30 aa SEQ ID NO: 1287 MAGE-3 segment 4 90 nts SEQ ID NO: 1288 Polypeptide encoded by SEQ ID NO: 1287 30 aa SEQ ID NO: 1289 MAGE-3 segment 5 90 nts SEQ ID NO: 1290 Polypeptide encoded by SEQ ID NO: 1289 30 aa SEQ ID NO: 1291 MAGE-3 segment 6 90 nts SEQ ID NO: 1292 Polypeptide encoded by SEQ ID NO: 1291 30 aa SEQ ID NO: 1293 MAGE-3 segment 7 90 nts SEQ ID NO: 1294 Polypeptide encoded by SEQ ID NO: 1293 30 aa SEQ ID NO: 1295 MAGE-3 segment 8 90 nts SEQ ID NO: 1296 Polypeptide encoded by SEQ ID NO: 1295 30 aa SEQ ID NO: 1297 MAGE-3 segment 9 90 nts SEQ ID NO: 1298 Polypeptide encoded by SEQ ID NO: 1297 30 aa SEQ ID NO: 1299 MAGE-3 segment 10 90 nts SEQ ID NO: 1300 Polypeptide encoded by SEQ ID NO: 1299 30 aa SEQ ID NO: 1301 MAGE-3 segment 11 90 nts SEQ ID NO: 1302 Polypeptide encoded by SEQ ID NO: 1301 30 aa SEQ ID NO: 1303 MAGE-3 segment 12 90 nts SEQ ID NO: 1304 Polypeptide encoded by SEQ ID NO: 1303 30 aa SEQ ID NO: 1305 MAGE-3 segment 13 90 nts SEQ ID NO: 1306 Polypeptide encoded by SEQ ID NO: 1305 30 aa SEQ ID NO: 1307 MAGE-3 segment 14 90 nts SEQ ID NO: 1308 Polypeptide encoded by SEQ ID NO: 1307 30 aa SEQ ID NO: 1309 MAGE-3 segment 15 90 nts SEQ ID NO: 1310 Polypeptide encoded by SEQ ID NO: 1309 30 aa SEQ ID NO: 1311 MAGE-3 segment 16 90 nts SEQ ID NO: 1312 Polypeptide encoded by SEQ ID NO: 1311 30 aa SEQ ID NO: 1313 MAGE-3 segment 17 90 nts SEQ ID NO: 1314 Polypeptide encoded by SEQ ID NO: 1313 30 aa SEQ ID NO: 1315 MAGE-3 segment 18 90 nts SEQ ID NO: 1316 Polypeptide encoded by SEQ ID NO: 1315 30 aa SEQ ID NO: 1317 MAGE-3 segment 19 90 nts SEQ ID NO: 1318 Polypeptide encoded by SEQ ID NO: 1317 30 aa SEQ ID NO: 1319 MAGE-3 segment 20 90 nts SEQ ID NO: 1320 Polypeptide encoded by SEQ ID NO: 1319 30 aa SEQ ID NO: 1321 MAGE-3 segment 21 54 nts SEQ ID NO: 1322 Polypeptide encoded by SEQ ID NO: 1321 18 aa SEQ ID NO: 1323 PRAME segment 1 90 nts SEQ ID NO: 1324 Polypeptide encoded by SEQ ID NO: 1323 30 aa SEQ ID NO: 1325 PRAME segment 2 90 nts SEQ ID NO: 1326 Polypeptide encoded by SEQ ID NO: 1325 30 aa SEQ ID NO: 1327 PRAME segment 3 90 nts SEQ ID NO: 1328 Polypeptide encoded by SEQ ID NO: 1327 30 aa SEQ ID NO: 1329 PRAME segment 4 90 nts SEQ ID NO: 1330 Polypeptide encoded by SEQ ID NO: 1329 30 aa SEQ ID NO: 1331 PRAME segment 5 90 nts SEQ ID NO: 1332 Polypeptide encoded by SEQ ID NO: 1331 30 aa SEQ ID NO: 1333 PRAME segment 6 90 nts SEQ ID NO: 1334 Polypeptide encoded by SEQ ID NO: 1333 30 aa SEQ ID NO: 1335 PRAME segment 7 90 nts SEQ ID NO: 1336 Polypeptide encoded by SEQ ID NO: 1335 30 aa SEQ ID NO: 1337 PRAME segment 8 90 nts SEQ ID NO: 1338 Polypeptide encoded by SEQ ID NO: 1337 30 aa SEQ ID NO: 1339 PRAME segment 9 90 nts SEQ ID NO: 1340 Polypeptide encoded by SEQ ID NO: 1339 30 aa SEQ ID NO: 1341 PRAME segment 10 90 nts SEQ ID NO: 1342 Polypeptide encoded by SEQ ID NO: 1341 30 aa SEQ ID NO: 1343 PRAME segment 11 90 nts SEQ ID NO: 1344 Polypeptide encoded by SEQ ID NO: 1343 30 aa SEQ ID NO: 1345 PRAME segment 12 90 nts SEQ ID NO: 1346 Polypeptide encoded by SEQ ID NO: 1345 30 aa SEQ ID NO: 1347 PRAME segment 13 90 nts SEQ ID NO: 1348 Polypeptide encoded by SEQ ID NO: 1347 30 aa SEQ ID NO: 1349 PRAME segment 14 90 nts SEQ ID NO: 1350 Polypeptide encoded by SEQ ID NO: 1349 30 aa SEQ ID NO: 1351 PRAME segment 15 90 nts SEQ ID NO: 1352 Polypeptide encoded by SEQ ID NO: 1351 30 aa SEQ ID NO: 1353 PRAME segment 16 90 nts SEQ ID NO: 1354 Polypeptide encoded by SEQ ID NO: 1353 30 aa SEQ ID NO: 1355 PRAME segment 17 90 nts SEQ ID NO: 1356 Polypeptide encoded by SEQ ID NO: 1355 30 aa SEQ ID NO: 1357 PRAME segment 18 90 nts SEQ ID NO: 1358 Polypeptide encoded by SEQ ID NO: 1357 30 aa SEQ ID NO: 1359 PRAME segment 19 90 nts SEQ ID NO: 1360 Polypeptide encoded by SEQ ID NO: 1359 30 aa SEQ ID NO: 1361 PRAME segment 20 90 nts SEQ ID NO: 1362 Polypeptide encoded by SEQ ID NO: 1361 30 aa SEQ ID NO: 1363 PRAME segment 21 90 nts SEQ ID NO: 1364 Polypeptide encoded by SEQ ID NO: 1363 30 aa SEQ ID NO: 1365 PRAME segment 22 90 nts SEQ ID NO: 1366 Polypeptide encoded by SEQ ID NO: 1365 30 aa SEQ ID NO: 1367 PRAME segment 23 90 nts SEQ ID NO: 1368 Polypeptide encoded by SEQ ID NO: 1367 30 aa SEQ ID NO: 1369 PRAME segment 24 90 nts SEQ ID NO: 1370 Polypeptide encoded by SEQ ID NO: 1369 30 aa SEQ ID NO: 1371 PRAME segment 25 90 nts SEQ ID NO: 1372 Polypeptide encoded by SEQ ID NO: 1371 30 aa SEQ ID NO: 1373 PRAME segment 26 90 nts SEQ ID NO: 1374 Polypeptide encoded by SEQ ID NO: 1373 30 aa SEQ ID NO: 1375 PRAME segment 27 90 nts SEQ ID NO: 1376 Polypeptide encoded by SEQ ID NO: 1375 30 aa SEQ ID NO: 1377 PRAME segment 28 90 nts SEQ ID NO: 1378 Polypeptide encoded by SEQ ID NO: 1377 30 aa SEQ ID NO: 1379 PRAME segment 29 90 nts SEQ ID NO: 1380 Polypeptide encoded by SEQ ID NO: 1379 30 aa SEQ ID NO: 1381 PRAME segment 30 90 nts SEQ ID NO: 1382 Polypeptide encoded by SEQ ID NO: 1381 30 aa SEQ ID NO: 1383 PRAME segment 31 90 nts SEQ ID NO: 1384 Polypeptide encoded by SEQ ID NO: 1383 30 aa SEQ ID NO: 1385 PRAME segment 32 90 nts SEQ ID NO: 1386 Polypeptide encoded by SEQ ID NO: 1385 30 aa SEQ ID NO: 1387 PRAME segment 33 90 nts SEQ ID NO: 1388 Polypeptide encoded by SEQ ID NO: 1387 30 aa SEQ ID NO: 1389 PRAME segment 34 54 nts SEQ ID NO: 1390 Polypeptide encoded by SEQ ID NO: 1389 18 aa SEQ ID NO: 1391 TRP21N2 segment 1 90 nts SEQ ID NO: 1392 Polypeptide encoded by SEQ ID NO: 1391 30 aa SEQ ID NO: 1393 TRP21N2 segment 2 90 nts SEQ ID NO: 1394 Polypeptide encoded by SEQ ID NO: 1393 30 aa SEQ ID NO: 1395 TRP21N2 segment 3 84 nts SEQ ID NO: 1396 Polypeptide encoded by SEQ ID NO: 1395 28 aa SEQ ID NO: 1397 NYNSO1a segment 1 90 nts SEQ ID NO: 1398 Polypeptide encoded by SEQ ID NO: 1397 30 aa SEQ ID NO: 1399 NYNSO1a segment 2 90 nts SEQ ID NO: 1400 Polypeptide encoded by SEQ ID NO: 1399 30 aa SEQ ID NO: 1401 NYNSO1a segment 3 90 nts SEQ ID NO: 1402 Polypeptide encoded by SEQ ID NO: 1401 30 aa SEQ ID NO: 1403 NYNSO1a segment 4 90 nts SEQ ID NO: 1404 Polypeptide encoded by SEQ ID NO: 1403 30 aa SEQ ID NO: 1405 NYNSO1a segment 5 90 nts SEQ ID NO: 1406 Polypeptide encoded by SEQ ID NO: 1405 30 aa SEQ ID NO: 1407 NYNSO1a segment 6 90 nts SEQ ID NO: 1408 Polypeptide encoded by SEQ ID NO: 1407 30 aa SEQ ID NO: 1409 NYNSO1a segment 7 90 nts SEQ ID NO: 1410 Polypeptide encoded by SEQ ID NO: 1409 30 aa SEQ ID NO: 1411 NYNSO1a segment 8 90 nts SEQ ID NO: 1412 Polypeptide encoded by SEQ ID NO: 1411 30 aa SEQ ID NO: 1413 NYNSO1a segment 9 90 nts SEQ ID NO: 1414 Polypeptide encoded by SEQ ID NO: 1413 30 aa SEQ ID NO: 1415 NYNSO1a segment 10 90 nts SEQ ID NO: 1416 Polypeptide encoded by SEQ ID NO: 1415 30 aa SEQ ID NO: 1417 NYNSO1a segment 11 90 nts SEQ ID NO: 1418 Polypeptide encoded by SEQ ID NO: 1417 30 aa SEQ ID NO: 1419 NYNSO1a segment 12 57 nts SEQ ID NO: 1420 Polypeptide encoded by SEQ ID NO: 1419 19 aa SEQ ID NO: 1421 NYNSO1b segment 1 90 nts SEQ ID NO: 1422 Polypeptide encoded by SEQ ID NO: 1421 30 aa SEQ ID NO: 1423 NYNSO1b segment 2 90 nts SEQ ID NO: 1424 Polypeptide encoded by SEQ ID NO: 1423 30 aa SEQ ID NO: 1425 NYNSO1b segment 3 90 nts SEQ ID NO: 1426 Polypeptide encoded by SEQ ID NO: 1425 30 aa SEQ ID NO: 1427 NYNSO1b segment 4 51 nts SEQ ID NO: 1428 Polypeptide encoded by SEQ ID NO: 1427 SEQ ID NO: 1429 LAGE1 segment 1 90 nts SEQ ID NO: 1430 Polypeptide encoded by SEQ ID NO: 1429 30 aa SEQ ID NO: 1431 LAGE1 segment 2 90 nts SEQ ID NO: 1432 Polypeptide encoded by SEQ ID NO: 1431 30 aa SEQ ID NO: 1433 LAGE1 segment 3 90 nts SEQ ID NO: 1434 Polypeptide encoded by SEQ ID NO: 1433 30 aa SEQ ID NO: 1435 LAGE1 segment 4 90 nts SEQ ID NO: 1436 Polypeptide encoded by SEQ ID NO: 1435 30 aa SEQ ID NO: 1437 LAGE1 segment 5 90 nts SEQ ID NO: 1438 Polypeptide encoded by SEQ ID NO: 1437 30 aa SEQ ID NO: 1439 LAGE1 segment 6 90 nts SEQ ID NO: 1440 Polypeptide encoded by SEQ ID NO: 1439 30 aa SEQ ID NO: 1441 LAGE1 segment 7 90 nts SEQ ID NO: 1442 Polypeptide encoded by SEQ ID NO: 1441 30 aa SEQ ID NO: 1443 LAGE1 segment 8 90 nts SEQ ID NO: 1444 Polypeptide encoded by SEQ ID NO: 1443 30 aa SEQ ID NO: 1445 LAGE1 segment 9 90 nts SEQ ID NO: 1446 Polypeptide encoded by SEQ ID NO: 1445 30 aa SEQ ID NO: 1447 LAGE1 segment 10 90 nts SEQ ID NO: 1448 Polypeptide encoded by SEQ ID NO: 1447 30 aa SEQ ID NO: 1449 LAGE1 segment 11 90 nts SEQ ID NO: 1450 Polypeptide encoded by SEQ ID NO: 1449 30 aa SEQ ID NO: 1451 LAGE1 segment 12 57 nts SEQ ID NO: 1452 Polypeptide encoded by SEQ ID NO: 1451 19 aa SEQ ID NO: 1453 Melanoma cancer specific Savine 10623 nts SEQ ID NO: 1454 Polypeptide encoded by SEQ ID NO: 1453 3541 aa SEQ ID NO: 1455 FIG. 16 A1S1 99mer 99 nts SEQ ID NO: 1456 FIG. 16 A1S2 100mer 100 nts SEQ ID NO: 1457 FIG. 16 A1S3 100mer 100 nts SEQ ID NO: 1458 FIG. 16 A1S4 100mer 100 nts SEQ ID NO: 1459 FIG. 16 A1S5 100mer 100 nts SEQ ID NO: 1460 FIG. 16 A1S6 99mer 99 nts SEQ ID NO: 1461 FIG. 16 A1S7 97mer 99 nts SEQ ID NO: 1462 FIG. 16 A1S8 100mer 100 nts SEQ ID NO: 1463 FIG. 16 A1S9 100mer 100 nts SEQ ID NO: 1464 FIG. 16 A1S10 75mer 76 nts SEQ ID NO: 1465 FIG. 16 A1F 20mer 20 nts SEQ ID NO: 1466 FIG. 16 A1R 20mer 20 nts SEQ ID NO: 1467 Amino acid sequence of immunostimulatory domain of an 16 aa invasin protein from Yersinia spp.

DETAILED DESCRIPTION OF THE INVENTION

1. Definitions

The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.

As used herein, the term “about” refers to a quantity, level, value, dimension, size, or amount that varies by as much as 30%, preferably by as much as 20%, and more preferably by as much as 10% to a reference quantity, level, value, dimension, size, or amount.

By “antigen-binding molecule” is meant a molecule that has binding affinity for a target antigen. It will be understood that this term extends to immunoglobulins, immunoglobulin fragments and non-immunoglobulin derived protein frameworks that exhibit antigen-binding activity.

The term “clade” as used herein refers to a hypothetical species of an organism and its descendants or a monophyletic group of organisms. Clades carry a definition, based on ancestry, and a diagnosis, based on synapomorphies. It should be noted that diagnoses of clades could change while definitions do not.

Throughout this specification, unless the context requires otherwise, the words “comprise”, “comprises” and “comprising” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements.

By “expression vector” is meant any autonomous genetic element capable of directing the synthesis of a protein encoded by the vector. Such expression vectors are known by practitioners in the art.

As used herein, the term “function” refers to a biological, enzymatic, or therapeutic function.

“Homology” refers to the percentage number of amino acids that are identical or constitute conservative substitutions as defined in Table B infra. Homology may be determined using sequence comparison programs such as GAP (Deveraux et al. 1984, Nucleic Acids Research 12, 387-395). In this way, sequences of a similar or substantially different length to those cited herein might be compared by insertion of gaps into the alignment, such gaps being determined, for example, by the comparison algorithm used by GAP.

To enhance an immune response (“immunoenhancement”), as is well-known in the art, means to increase an animal's capacity to respond to foreign or disease-specific antigens (e.g., cancer antigens) i.e., those cells primed to attack such antigens are increased in number, activity, and ability to detect and destroy the those antigens. Strength of immune response is measured by standard tests including: direct measurement of peripheral blood lymphocytes by means known to the art; natural killer cell cytotoxicity assays (see, e.g., Provinciali M. et al (1992, J. Immunol. Meth. 155: 19-24), cell proliferation assays (see, e.g., Vollenweider, I. and Groseurth, P. J. (1992, J. Immunol. Meth. 149: 133-135), immunoassays of immune cells and subsets (see, e.g. Loeffler, D. A., et al. (1992, Cytom. 13: 169-174); Rivoltini, L.; et al. (1992. Can. Immunol. Immunother. 34: 241-251); or skin tests for cell-mediated immunity (see, e.g., Chang, A. E. et al (1993, Cancer Res. 53: 1043-1050). Any statistically significant increase in strength of immune response as measured by the foregoing tests is considered “enhanced immune response” “immunoenhancement” or “immunopotentiation” as used herein. Enhanced immune response is also indicated by physical manifestations such as fever and inflammation, as well as healing of systemic and local infections, and reduction of symptoms in disease, i.e., decrease in tumour size, alleviation of symptoms of a disease or condition including, but not restricted to, leprosy, tuberculosis, malaria, naphthous ulcers, herpetic and papillomatous warts, gingivitis, artherosclerosis, the concomitants of AIDS such as Kaposi's sarcoma, bronchial infections, and the like. Such physical manifestations also define “enhanced immune response” “immunoenhancement” or “immunopotentiation” as used herein.

Reference herein to “immuno-interactive” includes reference to any interaction, reaction, or other form of association between molecules and in particular where one of the molecules is, or mimics, a component of the immune system.

By “isolated” is meant material that is substantially or essentially free from components that normally accompany it in its native state.

By “modulating” is meant increasing or decreasing, either directly or indirectly, an immune response against a target antigen of a member selected from the group consisting of a cancer and an organism, preferably a pathogenic organism.

By “natural gene” is meant a gene that naturally encodes a protein.

The term “natural polypeptide” as used herein refers to a polypeptide that exists in nature.

By “obtained from” is meant that a sample such as, for example, a polynucleotide extract or polypeptide extract is isolated from, or derived from, a particular source of the host. For example, the extract can be obtained from a tissue or a biological fluid isolated directly from the host.

The term “oligonucleotide” as used herein refers to a polymer composed of a multiplicity of nucleotide residues (deoxyribonucleotides or ribonucleotides, or related structural variants or synthetic analogues thereof) linked via phosphodiester bonds (or related structural variants or synthetic analogues thereof). Thus, while the term “oligonucleotide” typically refers to a nucleotide polymer in which the nucleotide residues and linkages between them are naturally occurring, it will be understood that the term also includes within its scope various analogues including, but not restricted to, peptide nucleic acids (PNAs), phosphoramidates, phosphorothioates, methyl phosphonates, 2-O-methyl ribonucleic acids, and the like. The exact size of the molecule can vary depending on the particular application. An oligonucleotide is typically rather short in length, generally from about 10 to 30 nucleotide residues, but the term can refer to molecules of any length, although the term “polynucleotide” or “nucleic acid” is typically used for large oligonucleotides.

By “operably linked” is meant that transcriptional and translational regulatory polynucleotides are positioned relative to a polypeptide-encoding polynucleotide in such a manner that the polynucleotide is transcribed and the polypeptide is translated.

The term “parent polypeptide” as used herein typically refers to a polypeptide encoded by a natural gene. However, it is possible that the parent polypeptide corresponds to a protein that is not naturally-occurring but has been engineered using recombinant techniques. In this instance, a polynucleotide encoding the parent polypeptide may comprise different but synonymous codons relative to a natural gene encoding the same polypeptide. Alternatively, the parent polypeptide may not correspond to a natural polypeptide sequence. For example, the parent polypeptide may comprise one or more consensus sequences common to a plurality of polypeptides.

The term “patient” refers to patients of human or other mammal and includes any individual it is desired to examine or treat using the methods of the invention. However, it will be understood that “patient” does not imply that symptoms are present. Suitable mammals that fall within the scope of the invention include, but are not restricted to, primates, livestock animals (e.g., sheep, cows, horses, donkeys, pigs), laboratory test animals (e.g., rabbits, mice, rats, guinea pigs, hamsters), companion animals (e.g., cats, dogs) and captive wild animals (e.g., foxes, deer, dingoes).

By “pharmaceutically-acceptable carrier” is meant a solid or liquid filler, diluent or encapsulating substance that can be safely used in topical or systemic administration to a mammal.

“Polypeptide”, “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues and to variants and synthetic analogues of the same. Thus, these terms apply to amino acid polymers in which one or more amino acid residues is a synthetic non-naturally occurring amino acid, such as a chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally-occurring amino acid polymers.

The term “polynucleotide” or “nucleic acid” as used herein designates mRNA, RNA, cRNA, cDNA or DNA. The term typically refers to oligonucleotides greater than 30 nucleotide residues in length.

By “primer” is meant an oligonucleotide which, when paired with a strand of DNA, is capable of initiating the synthesis of a primer extension product in the presence of a suitable polymerising agent. The primer is preferably single-stranded for maximum efficiency in amplification but can alternatively be double-stranded. A primer must be sufficiently long to prime the synthesis of extension products in the presence of the polymerisation agent. The length of the primer depends on many factors, including application, temperature to be employed, template reaction conditions, other reagents, and source of primers. For example, depending on the complexity of the target sequence, the oligonucleotide primer typically contains 15 to 35 or more nucleotide residues, although it can contain fewer nucleotide residues. Primers can be large polynucleotides, such as from about 35 nucleotides to several kilobases or more. Primers can be selected to be “substantially complementary” to the sequence on the template to which it is designed to hybridise and serve as a site for the initiation of synthesis. By “substantially complementary”, it is meant that the primer is sufficiently complementary to hybridise with a target polynucleotide. Preferably, the primer contains no mismatches with the template to which it is designed to hybridise but this is not essential. For example, non-complementary nucleotide residues can be attached to the 5′ end of the primer, with the remainder of the primer sequence being complementary to the template. Alternatively, non-complementary nucleotide residues or a stretch of non-complementary nucleotide residues can be interspersed into a primer, provided that the primer sequence has sufficient complementarity with the sequence of the template to hybridise therewith and thereby form a template for synthesis of the extension product of the primer.

“Probe” refers to a molecule that binds to a specific sequence or sub-sequence or other moiety of another molecule. Unless otherwise indicated, the term “probe” typically refers to a polynucleotide probe that binds to another polynucleotide, often called the “target polynucleotide”, through complementary base pairing. Probes can bind target polynucleotides lacking complete sequence complementarity with the probe, depending on the stringency of the hybridisation conditions. Probes can be labelled directly or indirectly.

By “recombinant polypeptide” is meant a polypeptide made using recombinant techniques, i.e., through the expression of a recombinant or synthetic polynucleotide.

Terms used to describe sequence relationships between two or more polynucleotides or polypeptides include “reference sequence”, “comparison window”, “sequence identity”, “percentage of sequence identity” and “substantial identity”. A “reference sequence” is at least 12 but frequently 15 to 18 and often at least 25 monomer units, inclusive of nucleotides and amino acid residues, in length. Because two polynucleotides may each comprise (1) a sequence (i.e., only a portion of the complete polynucleotide sequence) that is similar between the two polynucleotides, and (2) a sequence that is divergent between the two polynucleotides, sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a “comparison window” to identify and compare local regions of sequence similarity. A “comparison window” refers to a conceptual segment of at least 50 contiguous positions, usually about 50 to about 100, more usually about 100 to about 150 in which a sequence is compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. The comparison window may comprise additions or deletions (i.e., gaps) of about 20% or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Optimal alignment of sequences for aligning a comparison window may be conducted by computerised implementations of algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, Wis., USA) or by inspection and the best alignment (i.e., resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected. Reference also may be made to the BLAST family of programs as for example disclosed by Altschul et al., 1997, Nucl. Acids Res. 25:3389. A detailed discussion of sequence analysis can be found in Unit 19.3 of Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley & Sons Inc, 1994-1998, Chapter 15.

The term “sequence identity” as used herein refers to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis over a window of comparison. Thus, a “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, I) or the identical amino acid residue (e.g. Ala, Pro, Ser, Thr, Gly, Val, Leu, Ile, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gln, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. For the purposes of the present invention, “sequence identity” will be understood to mean the “match percentage” calculated by the DNASIS computer program (Version 2.5 for windows; available from Hitachi Software engineering Co., Ltd., South San Francisco, Calif., USA) using standard defaults as used in the reference manual accompanying the software.

The term “synthetic polynucleotide” as used herein refers to a polynucleotide formed in vitro by the manipulation of a polynucleotide into a form not normally found in nature. For example, the synthetic polynucleotide can be in the form of an expression vector. Generally, such expression vectors include transcriptional and translational regulatory polynucleotide operably linked to the polynucleotide.

The term “synonymous codon” as used herein refers to a codon having a different nucleotide sequence than another codon but encoding the same amino acid as that other codon.

By “translational efficiency” is meant the efficiency of a cell's protein synthesis machinery to incorporate the amino acid encoded by a codon into a nascent polypeptide chain. This efficiency can be evidenced, for example, by the rate at which the cell is able to synthesise the polypeptide from an RNA template comprising the codon, or by the amount of the polypeptide synthesised from such a template.

By “vector” is meant a polynucleotide molecule, preferably a DNA molecule derived, for example, from a plasmid, bacteriophage, yeast or virus, into which a polynucleotide can be inserted or cloned. A vector preferably contains one or more unique restriction sites and can be capable of autonomous replication in a defined host cell including a target cell or tissue or a progenitor cell or tissue thereof, or be integrable with the genome of the defined host such that the cloned sequence is reproducible. Accordingly, the vector can be an autonomously replicating vector, i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a linear or closed circular plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector can contain any means for assuring self-replication. Alternatively, the vector can be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. A vector system can comprise a single vector or plasmid, two or more vectors or plasmids, which together contain the total DNA to be introduced into the genome of the host cell, or a transposon. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. In the present case, the vector is preferably a viral or viral-derived vector, which is operably functional in animal and preferably mammalian cells. Such vector may be derived from a poxvirus, an adenovirus or yeast. The vector can also include a selection marker such as an antibiotic resistance gene that can be used for selection of suitable transformants. Examples of such resistance genes are known to those of skill in the art and include the nptII gene that confers resistance to the antibiotics kanamycin and G418 (Geneticin®) and the hph gene which confers resistance to the antibiotic hygromycin B.

2. Synthetic Polypeptides

The inventors have surprisingly discovered that the structure of a parent polypeptide can be disrupted sufficiently to impede, abrogate or otherwise alter at least one function of the parent polypeptide, while simultaneously minimising the destruction of potentially useful epitopes that are present in the parent polypeptide, by fusing, coupling or otherwise linking together different segments of the parent polypeptide in a different relationship relative to their linkage in the parent polypeptide. As a result of this change in relationship, the sequence of the linked segments in the resulting synthetic polypeptide is different to a sequence contained within the parent polypeptide. The synthetic polypeptides of the invention are useful as immunopotentiating agents, and are referred to elsewhere in the specification as scrambled antigen vaccines, super attenuated vaccines or “Savines”.

Thus, the invention broadly resides in a synthetic polypeptide comprising a plurality of different segments of at least one parent polypeptide, wherein said segments are linked together in a different relationship relative to their linkage in the at least one parent polypeptide.

It is preferable but not essential that the segments in said synthetic polypeptide are linked sequentially in a different order or arrangement relative to that of corresponding segments in said at least one parent polypeptide. For example, in the case of a parent polypeptide that comprises four contiguous or overlapping segments A-B-C-D, these segments may be linked in 23 other possible orders to form a synthetic polypeptide. These orders may be selected from the group consisting of: A-B-D-C, A-C-B-D, A-C-D-B, A-D-B-C, A-D-C-B, B-A-C-D, B-A-D-C, B-C-A-D, B-C-D-A, B-D-A-C, B-D-C-A, C-A-B-D, C-A-D-B, C-B-A-D, C-B-D-A, C-D-A-B, C-D-B-A, D-A-B-C, D-A-C-B, D-B-A-C, D-B-C-A, D-C-A-B, and D-C-B-A. Although the rearrangement of the segments is preferably random, it is especially preferable to exclude or otherwise minimize rearrangements that result in complete or partial reassembly of the parent sequence (e.g., ADBC, BACD, DABC). It will be appreciated, however, that the probability of such complete or partial reassembly diminishes as the number of segments for rearrangement increases.

The order of the segments is suitably shuffled, reordered or otherwise rearranged relative to the order in which they exist in the parent polypeptide so that the structure of the polypeptide is disrupted sufficiently to impede, abrogate or otherwise alter at least one function associated with the parent polypeptide. Preferably, the segments of the parent polypeptide are randomly rearranged in the synthetic polypeptide.

The parent polypeptide is suitably a polypeptide that is associated with a disease or condition. For example, the parent polypeptide may be a polypeptide expressed by a pathogenic organism or a cancer. Alternatively, the parent polypeptide can be a self peptide related to an autoimmune disease including, but are not limited to, diseases such as diabetes (e.g., juvenile diabetes), multiple sclerosis, rheumatoid arthritis, myasthenia gravis, atopic dermatitis, and psoriasis and ankylosing spondylitis. Accordingly, the synthetic molecules of the present invention may also have utility for the induction of tolerance in a subject afflicted with an autoimmune disease or condition or with an allergy or other condition to which tolerance is desired. For example tolerance may be induced by contacting an immature dendritic cell of the individual to be treated with a synthetic polypeptide of the invention or by expressing in an immature dendritic cell a synthetic polynucleotide of the invention. Tolerance may also be induced against antigens causing allergic responses (e.g., asthma, hay fever). In this case, the parent polypeptide is suitably an allergenic protein including, but not restricted to, house-dust-mite allergenic proteins as for example described by Thomas and Smith (1998, Allergy, 53(9): 821-832).

The pathogenic organism includes, but is not restricted to, yeast, a virus, a bacterium, and a parasite. Any natural host of the pathogenic organism is contemplated by the present invention and includes, but is not limited to, mammals, avians and fish. In a preferred embodiment, the pathogenic organism is a virus, which may be an RNA virus or a DNA virus. Preferably, the RNA virus is Human Immunodeficiency Virus (HIV), Poliovirus, and Influenza virus, Rous sarcoma virus, or a Flavivirus such as Japanese encephalitis virus. In a preferred embodiment, the RNA virus is a Hepatitis virus including, but not limited to, Hepatitis strains A, B and C. Suitably, the DNA virus is a Herpesvirus including, but not limited to, Herpes simplex virus, Epstein-Barr virus, Cytomegalovirus and Parvovirus. In a preferred embodiment, the virus is HIV and the parent polypeptide is suitably selected from env, gag, pol, vif, vpr, tat, rev, vpu and nef, or combination thereof. In an alternate preferred embodiment, the virus is Hepatitis C1a virus and the parent polypeptide is the Hepatitis C1a virus polyprotein.

In another embodiment, the pathogenic organism is a bacterium, which includes, but is not restricted to, Neisseria species, Meningococcal species, Haemophilus species Salmonella species, Streptococcal species, Legionella species and Mycobacterium species.

In yet another embodiment, the pathogenic organism is a parasite, which includes, but is not restricted to, Plasmodium species, Schistosoma species, Leishmania species, Trypanosoma species, Toxoplasma species and Giardia species.

Any cancer or tumour is contemplated by the present invention. For example, the cancer or tumour includes, but is not restricted to, melanoma, lung cancer, breast cancer, cervical cancer, prostate cancer, colon cancer, pancreatic cancer, stomach cancer, bladder cancer, kidney cancer, post transplant lymphoproliferative disease (PTLD), Hodgkin's Lymphoma and the like. Preferably, the cancer or tumour relates to melanoma. In a preferred embodiment of this type, the parent polypeptide is a melanocyte differentiation antigen which is suitably selected from gp100, MART, TRP-1, Tyros, TRP2, MC1R, MUC1F, MUC1R or a combination thereof In an alternate preferred embodiment of this type, the parent polypeptide is a melanoma-specific antigen which is suitably selected from BAGE, GAGE-1, gp100In4, MAGE-1, MAGE-3, PRAME, TRP2IN2, NYNSO1a, NYNSO1b, LAGE1 or a combination thereof.

In a preferred embodiment, the segments are selected on the basis of size. A segment according to the invention may be of any suitable size that can be utilised to elicit an immune response against an antigen encoded by the parent polypeptide. A number of factors can influence the choice of segment size. For example, the size of a segment should be preferably chosen such that it includes, or corresponds to the size of, T cell epitopes and their processing requirement. Practitioners in the art will recognise that class I-restricted T cell epitopes can be between 8 and 10 amino acids in length and if placed next to unnatural flanking residues, such epitopes can generally require 2 to 3 natural flanking amino acids to ensure that they are efficiently processed and presented. Class II-restricted T cell epitopes can range between 12 and 25 amino acids in length and may not require natural flanking residues for efficient proteolytic processing although it is believed that natural flanking residues may play a role. Another important feature of class II-restricted epitopes is that they generally contain a core of 9-10 amino acids in the middle which bind specifically to class II MHC molecules with flanking sequences either side of this core stabilising binding by associating with conserved structures on either side of class II MHC antigens in a sequence independent manner (Brown et al., 1993). Thus the functional region of class II-restricted epitopes is typically less than 15 amino acids long. The size of linear B cell epitopes and the factors effecting their processing, like class II-restricted epitopes, are quite variable although such epitopes are frequently smaller in size than 15 amino acids. From the foregoing, it is preferable, but not essential, that the size of the segment is at least 4 amino acids, preferably at least 7 amino acids, snore preferably at least 12 amino acids, more preferably at least 20 amino acids and more preferably at least 30 amino acids. Suitably, the size of the segment is less than 2000 amino acids, more preferably less than 1000 amino acids, more preferably less than 500 amino acids, more preferably less than 200 amino acids, more preferably less than 100 amino acids, more preferably less than 80 amino acids and even more preferably less than 60 amino acids and still even more preferably less than 40 amino acids. In this regard, it is preferable that the size of the segments is as small as possible so that the synthetic polypeptide adopts a functionally different structure relative to the structure of the parent polypeptide. It is also preferable that the size of the segments is large enough to minimise loss of T cell epitopes. In an especially preferred embodiment, the size of the segment is about 30 amino acids.

An optional spacer may be utilised to space adjacent segments relative to each other. Accordingly, an optional spacer may be interposed between some or all of the segments. The spacer suitably alters proteolytic processing and/or presentation of adjacent segment(s). In a preferred embodiment of this type, the spacer promotes or otherwise enhances proteolytic processing and/or presentation of adjacent segment(s). Preferably, the spacer comprises at least one amino acid. The at least one amino acid is suitably a neutral amino acid. The neutral amino acid is preferably alanine. Alternatively, the at least one amino acid is cysteine.

In a preferred embodiment, segments are selected such that they have partial sequence identity or homology with one or more other segments. Suitably, at one or both ends of a respective segment there is comprised at least 4 contiguous amino acids, preferably at least 7 contiguous amino acids, more preferably at least 10 contiguous amino acids, more preferably at least 15 contiguous amino acids and even more preferably at least 20 contiguous amino acids that are identical to, or homologous with, an amino acid sequence contained within one or more other of said segments. Preferably, at the or each end of a respective segment there is comprised less than 500 contiguous amino acids, more preferably less than 200 contiguous amino acids, more preferably less than 100 contiguous amino acids, more preferably less than 50 contiguous amino acids, more preferably less than 40 contiguous amino acids, and even more preferably less than 30 contiguous amino acids that are identical to, or homologous with, an amino acid sequence contained within one or more other of said segments. Such sequence overlap (also referred to elsewhere in the specification as “overlapping fragments” or “overlapping segments”) is preferable to ensure potential epitopes at segment boundaries are not lost and to ensure that epitopes at or near segment boundaries are processed efficiently if placed beside or near amino acids that inhibit processing. Preferably, the segment size is about twice the size of the overlap.

In a preferred embodiment, when segments have partial sequence homology therebetween, the homologous sequences suitably comprise conserved and/or non-conserved amino acid differences. Exemplary conservative substitutions are listed in the following table.

TABLE B Original Exemplary Residue Substitutions Ala Ser Arg Lys Asn Gln, His Asp Glu Cys Ser Gln Asn Glu Asp Gly Pro His Asn, Gln Ile Leu, Val Leu Ile, Val Lys Arg, Gln, Glu Met Leu, Ile, Phe Met, Leu, Tyr Ser Thr Thr Ser Trp Tyr Tyr Trp, Phe Val Ile, Leu

Conserved or non-conserved differences may correspond to polymorphisms in corresponding parent polypeptides. Polymorphic polypeptides are expressed by various pathogenic organisms and cancers. For example, the polymorphic polypeptides may be expressed by different viral strains or clades or by cancers in different individuals.

Sequence overlap between respective segments is preferable to minimise destruction of any epitope sequences that may result from any shuffling or rearrangement of the segments relative to their existing order in the parent polypeptide. If overlapping segments as described above are employed to form a synthetic polypeptide, it may not be necessary to change the order in which those segments are linked together relative to the order in which corresponding segments are normally present in the parent polypeptide. In this regard, such overlapping segments when linked together in the synthetic polypeptide can adopt a different structure relative to the structure of the parent polypeptide, wherein the different structure does not provide for one or more functions associated with the parent polypeptide. For example, in the case of four segments A-B-C-D each spanning 30 contiguous amino acids of the parent polypeptide and having a 10-amino acid overlapping sequence with one or more adjacent segments, the synthetic polypeptide will have duplicated 10-amino acid sequences bridging segments A-B, B-C and C-D. The presence of these duplicated sequences may be sufficient to render a different structure and to abrogate or alter function relative to the parent polypeptide.

In a preferred embodiment, segment size is about 30 amino acids and sequence overlap at one or both ends of a respective segment is about 15 amino acids. However, it will be understood that other suitable segment sizes and sequence overlap sizes are contemplated by the present invention, which can be readily ascertained by persons of skill in the art.

It is preferable but not necessary to utilise all the segments of the parent polypeptide in the construction of the synthetic polypeptide. Suitably, at least 30%, preferably at least 40%, more preferably at least 50%, even more preferably at least 60%, even more preferably at least 70%, even more preferably at least 80% and still even more preferably at least 90% of the parent polypeptide sequence is used in the construction of the synthetic polypeptide. However, it will be understood that the more sequence information from a parent polypeptide that is utilised to construct the synthetic polypeptide, the greater the population coverage will be of the synthetic polypeptide as an immunogen. Preferably, no sequence information from the parent polypeptide is excluded (e.g., because of an apparent lack of immunological epitopes).

Persons of skill in the art will appreciate that when preparing a synthetic polypeptide against a pathogenic organism (e.g., a virus) or a cancer, it may be preferable to use sequence information from a plurality of different polypeptides expressed by the organism or the cancer. Accordingly, in a preferred embodiment, segments from a plurality of different polypeptides are linked together to form a synthetic polypeptide according to the invention. It is preferable in this respect to utilise as many parent polypeptides as possible from, or in relation to, a particular source in the construction of the synthetic polypeptide. The source of parent polypeptides includes, but is not limited to, a pathogenic organism and a cancer. Suitably, at least about 30%, preferably at least 40%, more preferably at least 50%, even more preferably at least 60%, even more preferably at least 70%, even more preferably at least 80% and still even more preferably at least 90% of the parent polypeptides expressed by the source is used in the construction of the synthetic polypeptide. Preferably, parent polypeptides from a virus include, but are not restricted to, latent polypeptides, regulatory polypeptides or polypeptides expressed early during their replication cycle. Suitably, parent polypeptides from a parasite or bacterium include, but are not restricted to, secretory polypeptides and polypeptides expressed on the surface of the parasite or bacteria. It is preferred that parent polypeptides from a cancer or tumour are cancer specific polypeptides.

Suitably, hypervariable sequences within the parent polypeptide are excluded from the construction of the synthetic polypeptide.

The synthetic polypeptides of the inventions may be prepared by any suitable procedure known to those of skill in the art. For example, the polypeptide may be synthesised using solution synthesis or solid phase synthesis as described, for example, in Chapter 9 of Atherton and Shephard (1989, Solid Phase Peptide Synthesis: A Practical Approach. IRL Press, Oxford) and in Roberge et at (1995, Science 269: 202). Syntheses may employ, for example, either t-butyloxycarbonyl (t-Boc) or 9-fluorenylmethyloxycarbonyl (Fmoc) chemistries (see Chapter 9.1, of Coligan et al., CURRENT PROTOCOLS IN PROTEIN SCIENCE, John Wiley & Sons, Inc. 1995-1997; Stewart and Young, 1984, Solid Phase Peptide Synthesis, 2nd ed. Pierce Chemical Co., Rockford, Ill.; and Atherton and Shephard, supra).

Alternatively, the polypeptides may be prepared by a procedure including the steps of:

-   -   (a) preparing a synthetic construct including a synthetic         polynucleotide encoding a synthetic polypeptide wherein said         synthetic polynucleotide is operably linked to a regulatory         polynucleotide, wherein said synthetic polypeptide comprises a         plurality of different segments of a parent polypeptide, wherein         said segments are linked together in a different relationship         relative to their linkage in the parent polypeptide;     -   (b) introducing the synthetic construct into a suitable host         cell;     -   (c) culturing the host cell to express the synthetic polypeptide         from said synthetic construct; and     -   (d) isolating the synthetic polypeptide.

The synthetic construct is preferably in the form of an expression vector. For example, the expression vector can be a self-replicating extra-chromosomal vector such as a plasmid, or a vector that integrates into a host genome. Typically, the regulatory polynucleotide may include, but is not limited to, promoter sequences, leader or signal sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and termination sequences, and enhancer or activator sequences. Constitutive or inducible promoters as known in the art are contemplated by the invention. The promoters may be either naturally occurring promoters, or hybrid promoters that combine elements of more than one promoter. The regulatory polynucleotide will generally be appropriate for the host cell used for expression. Numerous types of appropriate expression vectors and suitable regulatory polynucleotides are known in the art for a variety of host cells.

In a preferred embodiment, the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selection genes are well known in the art and will vary with the host cell used.

The expression vector may also include a fusion partner (typically provided by the expression vector) so that the synthetic polypeptide of the invention is expressed as a fusion polypeptide with said fusion partner. The main advantage of fusion partners is that they assist identification and/or purification of said fusion polypeptide. In order to express said fusion polypeptide, it is necessary to ligate a polynucleotide according to the invention into the expression vector so that the translational reading frames of the fusion partner and the polynucleotide coincide.

Well known examples of fusion partners include, but are not limited to, glutathione-S-transferase (GST), Fc portion of human IgG, maltose binding protein (MBP) and hexahistidine (HIS₆), which are particularly useful for isolation of the fusion polypeptide by affinity chromatography. For the purposes of fusion polypeptide purification by affinity chromatography, relevant matrices for affinity chromatography are glutathione-, amylose-, and nickel- or cobalt-conjugated resins respectively. Many such matrices are available in “kit” form, such as the QIAexpress™ system (Qiagen) useful with (HIS₆) fusion partners and the Pharmacia GST purification system. In a preferred embodiment, the recombinant polynucleotide is expressed in the commercial vector pFLAG™.

Another fusion partner well known in the art is green fluorescent protein (GFP). This fusion partner serves as a fluorescent “tag” which allows the fusion polypeptide of the invention to be identified by fluorescence microscopy or by flow cytometry. The GFP tag is useful when assessing subcellular localisation of a fusion polypeptide of the invention, or for isolating cells which express a fusion polypeptide of the invention. Flow cytometric methods such as fluorescence activated cell sorting (FACS) are particularly useful in this latter application. Preferably, the fusion partners also have protease cleavage sites, such as for Factor X_(a), Thrombin and inteins (protein introns), which allow the relevant protease to partially digest the fusion polypeptide of the invention and thereby liberate the recombinant polypeptide of the invention therefrom. The liberated polypeptide can then be isolated from the fusion partner by subsequent chromatographic separation. Fusion partners according to the invention also include within their scope “epitope tags”, which are usually short peptide sequences for which a specific antibody is available. Well known examples of epitope tags for which specific monoclonal antibodies are readily available include c-Myc, influenza virus, haemagglutinin and FLAG tags. Alternatively, a fusion partner may be provided to promote other forms of immunity. For example, the fusion partner may be an antigen-binding molecule that is immuno-interactive with a conformational epitope on a target antigen or to a post-translational modification of a target antigen (e.g., an antigen-binding molecule that is immuno-interactive with a glycosylated target antigen).

The step of introducing the synthetic construct into the host cell may be effected by any suitable method including transfection, and transformation, the choice of which will be dependent on the host cell employed. Such methods are well known to those of skill in the art.

Synthetic polypeptides of the invention may be produced by culturing a host cell transformed with the synthetic construct. The conditions appropriate for protein expression will vary with the choice of expression vector and the host cell. This is easily ascertained by one skilled in the art through routine experimentation.

Suitable host cells for expression may be prokaryotic or eukaryotic. One preferred host cell for expression of a polypeptide according to the invention is a bacterium. The bacterium used may be Escherichia coli. Alternatively, the host cell may be an insect cell such as, for example, SF9 cells that may be utilised with a baculovirus expression system.

The synthetic polypeptide may be conveniently prepared by a person skilled in the art using standard protocols as for example described in Sambrook, et al., MOLECULAR CLONING. A LABORATORY MANUAL (Cold Spring Harbor Press, 1989), in particular Sections 16 and 17; Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (John Wiley & Sons, Inc. 1994-1998), in particular Chapters 10 and 16; and Coligan et al., CURRENT PROTOCOLS IN PROTEIN SCIENCE (John Wiley & Sons, Inc. 1995-1997), in particular Chapters 1, 5 and 6.

The amino acids of the synthetic polypeptide can be any non-naturally occurring or any naturally occurring amino acid. Examples of unnatural amino acids and derivatives during peptide synthesis include but are not limited to, use of 4-amino butyric acid, 6-aminohexanoic acid, 4-amino-3-hydroxy-5-phenylpentanoic acid, 4-amino-3-hydroxy-6-methylheptanoic acid, t-butylglycine, norleucine, norvaline, phenylglycine, ornithine, sarcosine, 2-thienyl alanine and/or D-isomers of amino acids. A list of unnatural amino acids contemplated by the present invention is shown in TABLE C.

TABLE C Non-conventional Amino Acid Non-conventional Amino Acid α-aminobutyric acid L-N-methylalanine α-amino-α-methylbutyrate L-N-methylarginine aminocyclopropane-carboxylate L-N-methylasparagine aminoisobutyric acid L-N-methylaspartic acid aminonorbornyl-carboxylate L-N-methylcysteine cyclohexylalanine L-N-methylglutamine cyclopentylalanine L-N-methylglutamic acid L-N-methylisoleucine L-N-methylhistidine D-alanine L-N-methylleucine D-arginine L-N-methyllysine D-aspartic acid L-N-methylmethionine D-cysteine L-N-methylnorleucine D-glutamate L-N-methylnorvaline D-glutamic acid L-N-methylornithine D-histidine L-N-methylphenylalanine D-isoleucine L-N-methylproline D-leucine L-N-methlylserine D-lysine L-N-methylthreonine D-methionine L-N-methyltryptophan D-ornithine L-N-methyltyrosine D-phenylalanine L-N-methylvaline D-proline L-N-methylethylglycine D-serine L-N-methyl-t-butylglycine D-threonine L-norleucine D-tryptophan L-norvaline D-tyrosine α-methyl-aminoisobutyrate D-valin α-methyl-γ-aminobutyrate D-α-methylalanine α-methylcyclohexylalanine D-α-methylarginine α-methylcylcopentylalanine D-α-methylasparagine α-methyl-α-napthylalanine D-α-methylaspartate α-methylpenicillamine D-α-methylcysteine N-(4-aminobutyl)glycine D-α-methylglutamine N-(2-aminoethyl)glycine D-α-methylhistidine N-(3-aminopropyl)glycine D-α-methylisoleucine N-amino-α-methylbutyrate D-α-methylleucine α-napthylalanine D-α-methyllysine N-benzylglycine D-α-methylmethionine N-(2-carbamylediyl)glycine D-α-methylornithiine N-(carbamylmethyl)glycine D-α-methylphenylalanine N-(2-carboxyethyl)glycine D-α-methylproline N-(carboxymethyl)glycine D-α-methylserine N-cyclobutylglycine D-α-methylthreonine N-cycloheptylglycine D-α-methyltryptophan N-cyclohexylglycine D-α-methyltyrosine N-cyclodecylglycine L-α-methylleucine L-α-methyllysine L-α-methylmethionine L-α-methylnorleucine L-α-methylnorvatine L-α-methylornithine L-α-methylphenylalanine L-α-methylproline L-α-methylserine L-α-methylthreonine L-α-methyltryptophan L-α-methyltyrosine L-α-methylvaline L-α-methylhomophenylalanine N-(N-(2,2-diphenylethyl N-(N-(3,3-diphenylpropyl carbamylmethyl)glycine carbamylmethyl)glycine 1-carboxy-1-(2,2-diphenyl-ethyl amino)cyclopropane

The invention also contemplates modifying the synthetic polypeptides of the invention using ordinary molecular biological techniques so as to alter their resistance to proteolytic degradation or to optimise solubility properties or to render them more suitable as an immunogenic agent.

3. Preparation of Synthetic Polynucleotides of the Invention

The invention contemplates synthetic polynucleotides encoding the synthetic polypeptides as for example described in Section 2 supra. Polynucleotides encoding segments of a parent polypeptide can be produced by any suitable technique. For example, such polynucleotides can be synthesised de novo using readily available machinery. Sequential synthesis of DNA is described, for example, in U.S. Pat. No 4,293,652. Instead of de novo synthesis, recombinant techniques may be employed including use of restriction endonucleases to cleave a polynucleotide encoding at least a segment of the parent polypeptide and use of ligases to ligate together in frame a plurality of cleaved polynucleotides encoding different segments of the parent polypeptide. Suitable recombinant techniques are described for example in the relevant sections of Ausubel, et al. (supra) and of Sambrook, et al., (supra) which are incorporated herein by reference. Preferably, the synthetic polynucleotide is constructed using splicing by overlapping extension (SOEing) as for example described by Horton et al. (1990, Biotechniques 8(5): 528-535; 1995, Mol Biotechnol. 3(2): 93-99; and 1997, Methods Mol Biol. 67: 141-149). However, it should be noted that the present invention is not dependent on, and not directed to, any one particular technique for constructing the synthetic construct.

Various modifications to the synthetic polynucleotides may be introduced as a means of increasing intracellular stability and half-life. Possible modifications include but are not limited to the addition of flanking sequences of ribo- or deoxy-nucleotides to the 5′ and/or 3′ ends of the molecule or the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages within the oligodeoxyribonucleotide backbone.

The invention therefore contemplates a method of producing a synthetic polynucleotide as broadly described above, comprising linking together in the same reading frame at least two nucleic acid sequences encoding different segments of a parent polypeptide to form a synthetic polynucleotide, which encodes a synthetic polypeptide according to the invention. Suitably, nucleic acid sequences encoding at least 10 segments, preferably at least 20 segments, more preferably at least 40 segments and more preferably at least 100 segments of a parent polypeptide are employed to produce the synthetic polynucleotide.

Preferably, the method further comprises selecting segments of the parent polypeptide, reverse translating the selected segments and preparing nucleic acid sequences encoding the selected segments. It is preferred that the method further comprises randomly linking the nucleic acid sequences together to form the synthetic polynucleotide. The nucleic acid sequences may be oligonucleotides or polynucleotides.

Suitably, segments are selected on the basis of size. Additionally, or in the alternative, segments are selected such that they have partial sequence identity or homology (i.e., sequence overlap) with one or more other segments. A number of factors can influence segment size and sequence overlap as mentioned above. In the case of sequence overlap, large amounts of duplicated nucleic acid sequences can sometimes result in sections of nucleic acid being lost during nucleic acid amplification (e.g., polymerase chain reaction, PCR) of such sequences, recombinant plasmid propagation in a bacterial host or during amplification of recombinant viruses containing such sequences. Accordingly, in a preferred embodiment, nucleic acid sequences encoding segments having sequence identity or homology with one or more other encoded segments are not linked together in an arrangement in which the identical or homologous sequences are contiguous. Also, it is preferable that different codons are used to encode a specific amino acid in a duplicated region. In this context, an amino acid of a parent polypeptide sequence is preferably reverse translated to provide a codon which, in the context of adjacent or local sequence elements, has a lower propensity of forming an undesirable sequence (e.g., a duplicated sequence or a palindromic sequence) that is refractory to the execution of a task (e.g., cloning or sequencing). Alternatively, segments may be selected such that they contain a carboxyl terminal leucine residue or such that reverse translated sequences encoding the segments contain restriction enzyme sites for convenient splicing of the reverse translated sequences.

The method optionally further comprises linking a spacer oligonucleotide encoding at least one spacer residue between segment-encoding nucleic acids. Such spacer residue(s) may be advantageous in ensuring that epitopes within the segments are processed and presented efficiently. Preferably, the spacer oligonucleotide encodes 2 to 3 spacer residues. The spacer residue is suitably a neutral amino acid, which is preferably alanine.

Optionally, the method further comprises linking in the same reading frame as other segment-containing nucleic acid sequences at least one variant nucleic acid sequence which encodes a variant segment having a homologous but not identical amino acid sequence relative to other encoded segments. Suitably, the variant segment comprises conserved and/or non-conserved amino acid differences relative to one or more other encoded segments. Such differences may correspond to polymorphisms as discussed above. In a preferred embodiment, degenerate bases are designed or built in to the at least one variant nucleic acid sequence to give rise to all desired homologous sequences.

When a large number of polymorphisms is intended to be covered, it is preferred that multiple synthetic polynucleotides are constructed rather than a single synthetic polynucleotide, which encodes all variant segments. For example, if there is less than 85% homology between polymorphic polypeptides, then it is preferred that more than one synthetic polynucleotide is constructed.

Preferably, the method further comprises optimising the codon composition of the synthetic polynucleotide such that it is translated efficiently by a host cell. In this regard, it is well known that the translational efficiency of different codons varies between organisms and that such differences in codon usage can be utilized to enhance the level of protein expression in a particular organism. In this regard, reference may be made to Seed et al. (International Application Publication No WO 96/09378) who disclose the replacement of existing codons in a parent polynucleotide with synonymous codons to enhance expression of viral polypeptides in mammalian host cells. Preferably, the first or second most frequently used codons are employed for codon optimization.

Preferably, gene splicing by overlap extension or “gene SOEing” (supra) is employed for the construction of the synthetic polynucleotide which is a PCR-based method of recombining DNA sequences without reliance on restriction sites and of directly generating mutated DNA fragments in vitro. By modifying the sequences incorporated into the 5′-ends of the primers, any pair of PCR products can be made to share a common sequence at one end. Under PCR conditions, the common sequence allows strands from two different fragments to hybridise to one another, forming an overlap. Extehsion of this overlap by DNA polymerase yields a recombinant molecule. However, a problem with long synthetic constructs is that mutations generally incorporate into amplified products during synthesis. In this instance, it is preferred that resolvase treatment is employed at various steps of the synthesis. Resolvases are bacteriophage-encoded endonucleases which recognise disruptions or mispairing of double stranded DNA and are primarily used by bacteriophages to resolve Holliday junctions (Mizuuchi, 1982; Youil et al., 1995). For example, T7 endonuclease I can be employed in synthetic DNA constructions to recognise mutations and cleave corrupted dsDNA. The mutated DNA strands are then hybridised to non-mutant or correct DNA sequences, which results in a mispairing of DNA bases. The mispaired bases are recognized by the resolvase, which then cleaves the DNA nearby leaving only correctly hybridised sequences intact. Preferably a thermostable resolvase enzyme is employed during splicing or amplification so that errors are not incorporated in downstream synthesis products.

Synthetic polynucleotides according to the invention can be operably linked to a regulatory polynucleotide in the form a synthetic construct as for example described in Section 2 supra. Synthetic constructs of the invention have utility inter alia as nucleic acid vaccines. The choice of regulatory polynucleotide and synthetic construct will depend on the intended host.

Exemplary expression vectors for expression of a synthetic polypeptide according to the invention include, but are not restricted to, modified Ankara Vaccinia virus as for example described by Allen et al. (2000, J. Immunol. 164(9): 4968-4978), fowlpox virus as for example described by Boyle and Coupar (1988, Virus Res. 10: 343-356) and the herpes simplex amplicons described for example by Fong et al. in U.S. Pat. No. 6,051,428. Alternatively, Adenovirus and Epstein-Barr virus vectors, which are preferably capable of accepting large amounts of DNA or RNA sequence information, can be used.

Preferred promoter sequences that can be utilized for expression of synthetic polypeptides include the P7.5 or PE/L promoters as for example disclosed by Kumar and Boyle. (1990, Virology 179:151-158), CMV and RSV promoters.

The synthetic construct optionally further includes a nucleic acid sequence encoding an immunostimulatory molecule. The immunostimulatory molecule may be fusion partner of the synthetic polypeptide. Alternatively, the immunostimulatory molecule may be translated separately from the synthetic polypeptide. Preferably, the immunostimulatory molecule comprises a general immunostimulatory peptide sequence. For example, the immunostimulatory peptide sequence may comprise a domain of an invasin protein (Inv) from the bacteria Yersinia spp as for example disclosed by Brett et al. (1993, Eur. J. Immunol. 23: 1608-1614). This immune stimulatory property results from the capability of this invasin domain to interact with the β1 integrin molecules present on T cells, particularly activated immune or memory T cells. A preferred embodiment of the invasin domain (Inv) for linkage to a synthetic polypeptide has been previously described in U.S. Pat. No. 5,759,551. The said Inv domain has the sequence: Thr-Ala-Lys-Ser-Lys-Lys-Phe-Pro-Ser-Tyr-Thr-Ala-Thr-Tyr-Gln-Phe [SEQ ID NO; 1467] or is an immune stimulatory homologue thereof from the corresponding region in another Yersinia species invasin protein. Such homologues thus may contain substitutions, deletions or insertions of amino acid residues to accommodate strain to strain variation, provided that the homologues retain immune stimulatory properties. The general immunostimulatory sequence may optionally be linked to the synthetic polypeptide by a spacer sequence.

In an alternate embodiment, the immunostimulatory molecule may comprise an immunostimulatory membrane or soluble molecule, which is suitably a T cell co-stimulatory molecule. Preferably, the T cell co-stimulatory molecule is a B7 molecule or a biologically active fragment thereof, or a variant or derivative of these. The B7 molecule includes, but is not restricted to, B7-1 and B7-2. Preferably, the B7 molecule is B7-1. Alternatively, the T cell co-stimulatory molecule may be an ICAM molecule such as ICAM-1 and ICAM-2.

In another embodiment, the immunostimulatory molecule can be a cytokine, which includes, but is not restricted to, an interleukin, a lymphokine, tumour necrosis factor and an interferon. Alternatively, the immunostimulatory molecule may comprise an immunomodulatory oligonucleotide as for example disclosed by Krieg in U.S. Pat. No. 6,008,200.

Suitably, the size of the synthetic polynucleotide does not exceed the ability of host cells to transcribe, translate or proteolytically process and present epitopes to the immune system. Practitioners in the art will also recognise that the size of the synthetic polynucleotide can impact on the capacity of an expression vector to express the synthetic polynucleotide in a host cell. In this connection, it is known that the efficacy of DNA vaccination reduces with expression vectors greater that 20-kb. In such situations it is preferred that a larger number of smaller synthetic constructs is utilized rather than a single large synthetic construct.

4. Immunopotentiating Compositions

The invention also contemplates a composition, comprising an immunopotentiating agent selected from the group consisting of a synthetic polypeptide as described in Section 2, and a synthetic polynucleotide or a synthetic construct as described in Section 3, together with a pharmaceutically acceptable carrier. One or more immunopotentiating agents can be used as actives in the preparation of immunopotentiating compositions. Such preparation uses routine methods known to persons skilled in the art. Typically, such compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. The preparation may also be emulsified. The active immunogenic ingredients are often mixed with excipients that are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants that enhance the effectiveness of the vaccine. Examples of adjuvants which may be effective include but are not limited to: aluminium hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thur-MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 1983A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion. For example, the effectiveness of an adjuvant may be determined by measuring the amount of antibodies resulting from the administration of the composition, wherein those antibodies are directed against one or more antigens presented by the treated cells of the composition.

The immunopotentiating agents may be formulated into a composition as neutral or salt forms. Pharmaceutically acceptable salts include the acid addition salts (formed with free amino groups of the peptide) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids such as acetic, oxalic, tartaric, maleic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic basis such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic basis as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.

If desired, devices or compositions containing the immunopotentiating agents suitable for sustained or intermittent release could be, in effect, implanted in the body or topically applied thereto for the relatively slow release of such materials into the body.

The compositions are conventionally administered parenterally, by injection, for example, either subcutaneously or intramuscularly. Additional formulations which are suitable for other modes of administration include suppositories and, in some cases, oral formulations. For suppositories, traditional binders and carriers may include, for example, polyalkylene glycols or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of 0.5% to 10%, preferably 1%-2%. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium carbonate, and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain 10%-95% of active ingredient, preferably 25%-70%.

Administration of the gene therapy construct to said mammal, preferably a human, may include delivery via direct oral intake, systemic injection, or delivery to selected tissue(s) or cells, or indirectly via delivery to cells isolated from the mammal or a compatible donor. An example of the latter approach would be stem cell therapy, wherein isolated stem cells having potential for growth and differentiation are transfected with the vector comprising the Sox18 nucleic acid. The stem cells are cultured for a period and then transferred to the mammal being treated.

With regard to nucleic acid based compositions, all modes of delivery of such compositions are contemplated by the present invention. Delivery of these compositions to cells or tissues of an animal may be facilitated by microprojectile bombardment, liposome mediated transfection (e.g., lipofectin or lipofectamine), electroporation, calcium phosphate or DEAE-dextran-mediated transfection, for example. In an alternate embodiment, a synthetic construct may be used as a therapeutic or prophylactic composition in the form of a “naked DNA” composition as is known in the art. A discussion of suitable delivery methods may be found in Chapter 9 of CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (Eds. Ausubel et al.; John Wiley & Sons Inc., 1997 Edition) or on the Internet site DNAvaccine.com. The compositions may be administered by intradermal (e.g., using panjet™ delivery) or intramuscular routes.

The step of introducing the synthetic polynucleotide into a target cell will differ depending on the intended use and species, and can involve one or more of non-viral and viral vectors, cationic liposomes, retroviruses, and adenoviruses such as, for example, described in Mulligan, R.C., (1993 Science 260 926-932) which is hereby incorporated by reference. Such methods can include, for example:

-   A. Local application of the synthetic polynucleotide by injection     (Wolff et al., 1990, Science 247 1465-1468, which is hereby     incorporated by reference), surgical implantation, instillation or     any other means. This method can also be used in combination with     local application by injection, surgical implantation, instillation     or any other means, of cells responsive to the protein encoded by     the synthetic polynucleotide so as to increase the effectiveness of     that treatment. This method can also be used in combination with     local application by injection, surgical implantation, instillation     or any other means, of another factor or factors required for the     activity of said protein. -   B. General systemic delivery by injection of DNA, (Calabretta et     al., 1993, Cancer Treat. Rev. 19 169-179, which is incorporated     herein by reference), or RNA, alone or in combination with liposomes     (Zhu et al., 1993, Science 261 209-212, which is incorporated herein     by reference), viral capsids or nanoparticles (Bertling et al.,     1991, Biotech. Appl. Biochem. 13 390-405, which is incorporated     herein by reference) or any other mediator of delivery. Improved     targeting might be achieved by linking the synthetic polynucleotide     to a targeting molecule (the so-called “magic bullet” approach     employing, for example, an antibody), or by local application by     injection, surgical implantation or any other means, of another     factor or factors required for the activity of the protein encoding     said synthetic polynucleotide , or of cells responsive to said     protein. -   C. Injection or implantation or delivery by any means, of cells that     have been modified ex vivo by transfection (for example, in the     presence of calcium phosphate: Chen et al., 1987, Mole. Cell     Biochem. 7 2745-2752, or of cationic lipids and polyamines: Rose et     al., 1991, BioTech. 10 520-525, which articles are incorporated     herein by reference), infection, injection, electroporation     (Shigekawa et al., 1988, BioTech. 6 742-751, which is incorporated     herein by reference) or any other way so as to increase the     expression of said synthetic polynucleotide in those cells. The     modification can be mediated by plasmid, bacteriophage, cosmid,     viral (such as adenoviral or retroviral; Mulligan, 1993, Science 260     926-932; Miller, 1992, Nature 357 455-460; Salmons et al., 1993,     Hum. Gen. Ther. 4 129-141, which articles are incorporated herein by     reference) or other vectors, or other agents of modification such as     liposomes (Zhu et al., 1993, Science 261 209-212, which is     incorporated herein by reference), viral capsids or nanoparticles     (Bertling et al., 1991, Biotech. Appl. Biochem. 13 390-405, which is     incorporated herein by reference), or any other mediator of     modification. The use of cells as a delivery vehicle for genes or     gene products has been described by Barr et al., 1991, Science 254     1507-1512 and by Dhawan et al., 1991, Science 254 1509-1512, which     articles are incorporated herein by reference. Treated cells can be     delivered in combination with any nutrient, growth factor, matrix or     other agent that will promote their survival in the treated subject.

Also encapsulated by the present invention is a method for treatment and/or prophylaxis of a disease or condition, comprising administering to a patient in need of such treatment a therapeutically effective amount of a composition as broadly described above. The disease or condition may be caused by a pathogenic organism or a cancer as for example described above.

In a preferred embodiment, the immunopotentiating composition of the invention is suitable for treatment of, or prophylaxis against, a cancer. Cancers which could be suitably treated in accordance with the practices of this invention include cancers of the lung, breast, ovary, cervix, colon, head and neck, pancreas, prostate, stomach, bladder, kidney, bone liver, oesophagus, brain, testicle, uterus, melanoma and the various leukemias and lymphomas.

In an alternate embodiment, the immunopotentiating composition is suitable for treatment of, or prophylaxis against, a viral, bacterial or parasitic infection. Viral infections contemplated by the present invention include, but are not restricted to, infections caused by HIV, Hepatitis, Influenza, Japanese encephalitis virus, Epstein-Barr virus and respiratory syncytial virus. Bacterial infections include, but are not restricted to, those caused by Neisseria species, Meningococcal species, Haemophilus species Salmonella species, Streptococcal species, Legionella species and Mycobacterium species. Parasitic infections encompassed by the invention include, but are not restricted to, those caused by Plasmodium species, Schistosoma species, Leishmania species, Trypanosoma species, Toxoplasma species and Giardia species.

The above compositions or vaccines may be administered in a manner compatible with the dosage formulation, and in such amount as is therapeutically effective to alleviate patients from the disease or condition or as is prophylactically effective to prevent incidence of the disease or condition in the patient. The dose administered to a patient, in the context of the present invention, should be sufficient to effect a beneficial response in a patient over time such as a reduction or cessation of blood loss. The quantity of the composition or vaccine to be administered may depend on the subject to be treated inclusive of the age, sex, weight and general health condition thereof. In this regard, precise amounts of the composition or vaccine for administration will depend on the judgement of the practitioner. In determining the effective amount of the composition or vaccine to be administered in the treatment of a disease or condition, the physician may evaluate the progression of the disease or condition over time. In any event, those of skill in the art may readily determine suitable dosages of the composition or vaccine of the invention.

In a preferred embodiment, DNA-based immunopotentiating agent (e.g., 100 μg) is delivered intradermally into a patient at day 1 and at week 8 to prime the patient. A recombinant poxvirus (e.g., at 10⁷ pfu/mL) from which substantially the same immunopotentiating agent can be expressed is then delivered intradermally as a booster at weeks 16 and 24, respectively.

The effectiveness of the immunisation may be assessed using any suitable technique. For example, CTL lysis assays may be employed using stimulated splenocytes or peripheral blood mononuclear cells (PBMC) on peptide coated or recombinant virus infected cells using ⁵¹Cr labelled target cells. Such assays can be performed using for example primate, mouse or human cells (Allen et al., 2000, J. Immunol. 164(9): 4968-4978 also Woodberry et al., infra). Alternatively, the efficacy of the immunisation may be monitored using one or more techniques including, but not limited to, HLA class I Tetramer staining—of both fresh and stimulated PBMCs (see for example Allen et al., supra), proliferation assays (Allen et al., supra), Elispot™ Assays and intracellular INF-gamma staining (Allen et al., supra), ELISA Assays—for linear B cell responses; and Western blots of cell sample expressing the synthetic polynucleotides.

5. Computer Related Embodiments

The design or construction of a synthetic polypeptide sequence or a synthetic polynucleotide sequence according to the invention is suitably facilitated with the assistance of a computer programmed with software, which inter alia fragments a parent sequence into fragments, and which links those fragments together in a different relationship relative to their linkage in the parent sequence. The ready use of a parent sequence for the construction of a desired synthetic molecule according to the invention requires that it be stored in a computer-readable format. Thus, in accordance with the present invention, sequence data relating to a parent molecule (e.g. a parent polypeptide) is stored in a machine-readable storage medium, which is capable of processing the data to fragment the sequence of the parent molecule into fragments and to link together the fragments in a different relationship relative to their linkage in the parent molecule.

Therefore, another embodiment of the present invention provides a machine-readable data storage medium, comprising a data storage material encoded with machine readable data which, when used by a machine programmed with instructions for using said data, fragments a parent sequence into fragments, and links those fragments together in a different relationship relative to their linkage in the parent sequence. In a preferred embodiment of this type, a machine-readable data storage medium is provided that is capable of reverse translating the sequence of a respective fragment to provide a nucleic acid sequence encoding the fragment and to link together in the same reading frame each of the nucleic acid sequences to provide a polynucleotide sequence that codes for a polypeptide sequence in which said fragments are linked together in a different relationship relative to their linkage in a parent polypeptide sequence.

In another embodiment, the invention encompasses a computer for designing the sequence of a synthetic polypeptide and/or a synthetic polynucleotide of the invention, wherein the computer comprises wherein said computer comprises: (a) a machine readable data storage medium comprising a data storage material encoded with machine readable data, wherein said machine readable data comprises the sequence of a parent polypeptide; (b) a working memory for storing instructions for processing said machine-readable data; (c) a central-processing unit coupled to said working memory and to said machine-readable data storage medium, for processing said machine-readable data into said synthetic polypeptide sequence and/or said synthetic polynucleotide; and (d) an output hardware coupled to said central processing unit, for receiving said synthetic polypeptide sequence and/or said synthetic polynucleotide.

In yet another embodiment, the invention contemplates a computer program product for designing the sequence of a synthetic polynucleotide of the invention, comprising code that receives as input the sequence of a parent polypeptide, code that fragments the sequence of the parent polypeptide into fragments, code that reverse translates the sequence of a respective fragment to provide a nucleic acid sequence encoding the fragment, code that links together in the same reading frame each said nucleic acid sequence to provide a polynucleotide sequence that codes for a polypeptide sequence in which said fragments are linked together in a different relationship relative to their linkage in the parent polypeptide sequence, and a computer readable medium that stores the codes.

A version of these embodiments is presented in FIG. 23, which shows a system 10 including a computer 11 comprising a central processing unit (“CPU”) 20, a working memory 22 which may be, e.g., RAM (random-access memory) or “core” memory, mass storage memory 24 (such as one or more disk drives or CD-ROM drives), one or more cathode-ray tube (“CRT”) display terminals 26, one or more keyboards 28, one or more input lines 30, and one or more output lines 40, all of which are interconnected by a conventional bidirectional system bus 50.

Input hardware 36, coupled to computer 11 by input lines 30, may be implemented in a variety of ways. For example, machine-readable data of this invention may be inputted via the use of a modem or modems 32 connected by a telephone line or dedicated data line 34. Alternatively or additionally, the input hardware 36 may comprise CD. Alternatively, ROM drives or disk drives 24 in conjunction with display terminal 26, keyboard 28 may also be used as an input device.

Output hardware 46, coupled to computer 11 by output lines 40, may similarly be implemented by conventional devices. By way of example, output hardware 46 may include CRT display terminal 26 for displaying a synthetic polynucleotide sequence or a synthetic polypeptide sequence as described herein. Output hardware might also include a printer 42, so that hard copy output may be produced, or a disk drive 24, to store system output for later use.

In operation, CPU 20 coordinates the use of the various input and output devices 36,46 coordinates data accesses from mass storage 24 and accesses to and from working memory 22, and determines the sequence of data processing steps. A number of programs may be used to process the machine readable data of this invention. Exemplary programs may use for example the steps outlined in the flow diagram illustrated in FIG. 24. Broadly, these steps include (1) inputting at least one parent polypeptide sequence; (2) optionally adding to alanine spacers at the ends of each polypeptide sequence; (3) fragmenting the polypeptide sequences into fragments (e.g., 30 amino acids long), which are preferably overlapping (e.g., by 15 amino acids); (4) reverse translating the fragment to provide a nucleic acid sequence for each fragment and preferably using for the reverse translation first and second most translationally efficient codons for a cell type, wherein the codons are preferably alternated out of frame with each other in the overlaps of consecutive fragments; (5) randomly rearranging the fragments; (6) checking whether rearranged fragments recreate at least a portion of a parent polypeptide sequence; (7) repeating randomly rearranging the fragments when rearranged fragments recreate said at least a portion; or otherwise (8) linking the rearranged fragments together to produce a synthetic polypeptide sequence and/or a synthetic polynucleotide sequence; and (9) outputting said synthetic polypeptide sequence and/or a synthetic polynucleotide sequence. An example of an algorithm which uses inter alia the aforementioned steps is shown in FIG. 25. By way of example, this algorithm has been used for the design of synthetic polynucleotides and synthetic polypeptides according to the present invention for Hepatitis C1a and for melanoma, as illustrated in FIGS. 26 and 27.

FIG. 28 shows a cross section of a magnetic data storage medium 100 which can be encoded with machine readable data, or set of instructions, for designing a synthetic molecule of the invention, which can be carried out by a system such as system 10 of FIG. 23. Medium 100 can be a conventional floppy diskette or hard disk, having a suitable substrate 101, which may be conventional, and a suitable coating 102, which may be conventional, on one or both sides, containing magnetic domains (not visible) whose polarity or orientation can be altered magnetically. Medium 100 may also have an opening (not shown) for receiving the spindle of a disk drive or other data storage device 24. The magnetic domains of coating 102 of medium 100 are polarised or oriented so as to encode in manner which may be conventional, machine readable data such as that described herein, for execution by a system such as system 10 of FIG. 23.

FIG. 29 shows a cross section of an optically readable data storage medium 110 which also can be encoded with such a machine-readable data, or set of instructions, for designing a synthetic molecule of the invention, which can be carried out by a system such as system 10 of FIG. 23. Medium 110 can be a conventional compact disk read only memory (CD-ROM) or a rewritable medium such as a magneto-optical disk, which is optically readable and magneto-optically writable. Medium 100 preferably has a suitable substrate 111, which may be conventional, and a suitable coating 112, which may be conventional, usually of one side of substrate 111.

In the case of CD-ROM, as is well known, coating 112 is reflective and is impressed with a plurality of pits 113 to encode the machine-readable data. The arrangement of pits is read by reflecting laser light off the surface of coating 112. A protective coating 114, which preferably is substantially transparent, is provided on top of coating 112.

In the case of a magneto-optical disk, as is well known, coating 112 has no pits 113, but has a plurality of magnetic domains whose polarity or orientation can be changed magnetically when heated above a certain temperature, as by a laser (not shown). The orientation of the domains can be read by measuring the polarisation of laser light reflected from coating 112. The arrangement of the domains encodes the data as described above.

In order that the invention may be readily understood and put into practical effect, particular preferred non-limiting embodiments will now be described as follows.

EXAMPLES Example 1 Preparation of an HIV Savine Experimental Protocol

Plasmids

The plasmid pDNAVacc is ampicillin resistant and contains an expression cassette comprising a CMV promoter and enhancer, a synthetic intron, a multiple cloning site (MCS) and a SV40poly A signal sequence (Thomson et al., 1998). The plasmid pTK7.5 and contains a selection cassette, a pox virus 7.5 early/late promoter and a MCS flanked on either side by Vaccinia virus TK gene sequences.

Recombinant Vaccinia Viruses

Recombinant Vaccinia viruses expressing the gag, env (IIB) and pol (LAI) genes of HIV-1 were used as previously described and denoted VV-GAG, VV-POL, VV-ENV (Woodberry et al., 1999; Kent et al., 1998).

Marker Rescue Recombination

Recombinant Vaccinia viruses containing Savine constructs were generated by marker rescue recombination, using protocols described previously (Boyle et al., 1985). Plaque purified viruses were tested for the TK phenotype and for the appropriate genome arrangement by Southern blot and PCR.

Oligonucleotides

Oligonucleotides 50 nmol scale and desalted were purchased from Life Technologies. Short oligonucleotides were resuspended in 100 μL of water, their concentration determined, then diluted to 20 μM for use in PCR or sequencing reactions. Long oligonucleotides for splicing reactions were denatured for 5 minutes at 94° C. in 20 μL of formamide loading buffer then 0.5 μL gel purified on a 6% polyacrylamide gel. Gel slices containing full-length oligonucleotides were visualised with ethidium bromide, excised, placed in Eppendorf™ tubes, combined with 200 μL of water before being crushed using the plunger of a 1 mL syringe. Before being used in splicing reactions the crushed gel was resuspended in an appropriate volume of buffer and 1-2 μL of the resuspendate used directly in the splicing reactions.

Sequencing

Sequencing was performed using Dye terminator sequencing reactions and analyzed by the Biomedical Resource Facility at the John Curtin School of Medical Research using an ABI automated sequencer.

Restimulation of Lymphocytes from HIV Infected Patients

Two pools of recombinant Vaccinia viruses containing VV-AC1+VV-BC1 (Pool 1) or VV-AC2+VV-BC2+VV-CC2 (Pool 2) were used to restimulate lymphocytes from the blood samples of HIV-infected patients. Briefly CTL lines were generated from HIV-infected donor PBMC. A fifth of the total PBMC were infected with either Pool 1 or Pool 2 Vaccinia viruses then added back to the original cell suspension. The infected cell suspension was then cultured with IL-7 for 1 week.

CTL Assays

Restimulated PBMCs were used as effectors in a standard ⁵¹Cr-release CTL assay. Targets were autologous EBV-transformed lymphoblastoid cell lines (LCLs) infected with the following viruses: Pool 1, Pool 2, VV-GAG, VV-POL or VV-ENV. Assay controls included uninfected targets, targets infected with VV-lacZ (virus control) and K562 cells.

Results

HIV Savine Design

A main goal of the Savine strategy is to include as much protein sequence information from a pathogen or cancer as possible in such a way that potential T cell epitopes remain intact and so that the vaccine or therapy is extremely safe. An HIV Savine is described herein not only to compare this strategy to other strategies but also, to produce an HIV vaccine that would provide the maximum possible population coverage as well as catering for the major HIV clades.

A number of design criteria was first determined to exploit the many advantages of using a synthetic approach. One advantage is that it is possible to use consensus protein sequences to design these vaccines. Using consensus sequences for a highly variable virus like HIV should provide better vaccine coverage because individual viral isolate sequences may have lost epitopes which induce CTL against the majority of other viral isolates. Thus, using the-consensus sequences of each HIV lade rather than individual isolate sequences should provide better vaccine coverage. Taking this one step further, a consensus sequence that covers all HIV clades should theoretically provide better coverage than using just the consensus sequences for individual clades. Before designing such a sequence however, it was decided that a more appropriate and focussed HIV vaccine might be constructed if the various clades were first ranked according to their relative importance. To establish such a ranking the following issues were considered, current prevalence of each lade, the rate at which each lade is increasing and the capacity of various regions of the world to cope with the HIV pandemic (FIGS. 1 and 2). These criteria produced the following ranking, Clade E≧clade A>clade C>clade B>cldade D>other clades. Clades E and A were considered to almost equal since they are very similar except in their envelope protein sequences, which differ considerably.

Another advantage of synthesising a designed sequence is that it is possible to incorporate degenerate sequences into their design. In the case of HIV, this means that more than one amino acid can be included at various positions to improve the ability of the vaccine to cater for the various HIV clades and isolates. Coverage is improved because mutations in different HIV clades and also in individual isolate sequences, while mostly destroying specific T cell epitopes, can result in the formation of new potentially useful epitopes nearby (Goulder et al., 1997). Incorporating degenerate amino acid sequences, however, also means that more than one construct must be made and mixed together. The number of constructs required depends on the frequency with which mutations are incorporated into the design. While this approach requires the construction of additional constructs, these constructs can be prepared from the same set of degenerate long oligonucleotides, significantly reducing the cost of providing such considerable interclade coverage.

A set of degeneracy rules was developed for the incorporation of amino acid mutations into the design which meant that a maximum of eight constructs would be required so that theoretically all combinations were present, as follows: 1) Two amino acids at three positions (or less) within any group of nine amino acids (i.e., present in a CTL epitope); 2) Three amino acids at one position and two at another (or not) within any group of nine amino acids; 3) Four amino acids at one position and two at another (or not) within any group of nine amino acids. The reason why these rules were applied to nine amino acids (the average CTL epitope size) and not to larger stretches of amino acid sequence to cater for class II restricted epitopes, is because class II-restricted epitopes generally have a core sequence of nine amino acids in the middle which bind specifically to class II MHC molecules with the extra flanking sequences stabilising binding, by associating with either side of class II MHC antigens in a largely sequence independent manner (Brown et al., 1993).

Using the HIV clade ranking described above, the amino acid degeneracy rules and in some situations the similarity between amino acids, a degenerate consensus protein sequence was designed for each HIV protein using the consensus protein sequences for Molecular Immunology Database, 1997). It is important to note that in some situations the order with which each of the above design criteria was applied was altered. Each time this was done the primary goal however was to increase the ability of the Savine to cater for interclade differences. Two isolate sequences, GenBank accession U51189 and U46016, for lade E and lade C, respectively, were used when a consensus sequence for some HIV proteins from these two clades was unavailable (Gao et al., 1996; Salminen et al., 1996). The design of a consensus sequence for the hypervariable regions of the HIV envelope protein and in some cases between these regions (hypervariable regions 1-2 and 3-5) was difficult and so these regions were excluded from the vaccine design.

Once a degenerate consensus sequence was designed for each HIV protein, an approach was then determined for incorporating all the protein sequences safely into the vaccine. One convenient approach to ensure that a vaccine will be safe is to systematically fragment and randomly rearrange the protein sequences together thus abrogating or otherwise altering their structure and function. The protein sequences still have to be immunologically functional however, meaning that the process used to fragment the sequences should not destroy potential epitopes. To decide on the best approach for systematically fragmenting protein sequences, the main criteria used was the size of T epitopes and their processing requirements. Class I-restricted T cell epitopes are 8-10 amino acids long and generally require 2-3 natural flanking amino acids to ensure their efficient processing and presentation if placed next to unnatural flanking residues (Del Val et al., 1991; Thomson et al., 1995). Class II-restricted T cell epitopes range between 12-25 amino acids long and do appear to require natural flanking residues for processing however, it is difficult to rule out a role for natural flanking residues in all cases due to the complexity of their processing pathways (Thomson et al., 1998). Also class II-restricted epitopes despite being larger than CTL epitopes generally have a core sequence of 9-10 amino acids, which binds to MHC molecules in a sequence specific fashion. Thus, based on current knowledge, it was decided that an advantageous approach was to overlap the fragments by at least 15 amino acids to ensure that potential epitopes which might lie across fragment boundaries are not lost and to ensure that CTL epitopes near fragment boundaries, that are placed beside or near inhibitory amino acids in adjacent fragments, are processed efficiently. In deciding the optimal fragment size, the main criteria used were that size had to be small enough to cause the maximum disruption to the structure and function of proteins but large enough to cover the sequence information as efficiently as possible without any further unnecessary duplication. Based on these criteria the fragments would be twice the overlap size, in this case 30 amino acids long.

The designed degenerate protein sequences were then separated into fragments 30 amino acid long and overlapping by fifteen amino acids. Two alanine amino acids were also added to the start and end of the first and last fragment for each protein or envelop protein segment to ensure these fragments were not placed directly adjacent to amino acids capable of blocking epitope processing (Del Val et al., 1991). The next step was to reverse translate each protein sequence back into DNA. Duplicating DNA sequences was avoided when constructing DNA sequences encoding a tandem repeat of identical or homologous amino acid sequences to maximise expression of the Savine. In this regard, the first and second most commonly used mammalian codons (shown in FIG. 12) were assigned to amino acids in these repeat regions, wherein a first codon was used to encode an amino acid in one of the repeated sequences and wherein a second but synonymous codon was used for the other repeated sequence (e.g., see the gag HIV protein in FIG. 13). To cater for the designed amino acid mutations more than one base was assigned to some positions using the IUPAC DNA codes without exceeding more than three base variations (eight possible combinations) in any group of 27 bases (FIG. 12). Where a particular combination of amino acids could not be incorporated, because too many degenerate bases would be required, some or all of the amino acid degeneracy was removed according to the protein consensus design rules outlined above. Also the degenerate codons were checked to determine if they could encode a stop codon, if stop codons could not be avoided then the amino acid degeneracy was also simplified again according to the protein consensus design rules outlined above.

The designed DNA segments were then scrambled randomly and joined to create twenty-two subcassettes approximately 840 bp in size. Extra DNA sequences incorporating sites for one of the cohesive restriction enzymes XbaI, SpeI, AvrII or NheI and 3 additional base pairs (to cater for premature Taq polymerase termination) were then added to each end of each subcassette (FIG. 14). Some of these extra DNA sequences also contained, the cohesive restriction sites for SalI or XhoI, Kozak signal sequences and start or stop codons to enable the subcassettes to be joined and expressed either as three large cassettes or one full length protein (FIGS. 14 and 15).

In designing the HIV Savine one issue that required investigation was whether such a large DNA molecule would be fully expressed and Whether epitopes encoded near the end of the molecule would be efficiently presented to the immune system. The inventors also wished to show that mixing two or more degenerate Savine constructs together could induce T cell responses that recognise mutated sequences. To examine both issues DNA coding for a degenerate murine influenza nucleoprotein CTL epitope, NP365-373, which differs by two amino acids at positions 71 and 72 in influenza strain A/PR/8/34 compared to the A/NT/60/68 strain and restricted by H2-Db, was inserted before the last stop codon at the end of the HIV Savine design (FIG. 15). An important and unusual characteristic of both of these naturally occurring NP365-373 sequences, which enabled the present inventors to examine the effectiveness of incorporating mutated sequences, is that they generate CTL responses which do not cross react with the alternate sequence (Townsend et. al., 1986). This is an unusual characteristic because epitopes not destroyed by mutation usually induce CTL responses that cross-react.

Up to ten long oligonucleotides up to 100 bases long and two short amplification oligonucleotides were synthesized to enable construction of each subcassette (Life Technologies). In designing each oligonucleotide the 3′ end and in most cases also the 5′ end had to be either a ‘c’ or a ‘g’ to ensure efficient extension during PCR splicing. The overlap region for each long oligonucleotide was designed to be at least 16 bp with approximately 50% G/C content. Also oligonucleotide overlaps were not placed where degenerate DNA bases coded for degenerate amino acids to avoid splicing difficulties later. Where this was too difficult some degenerate bases were removed according to the protein consensus design rules outlined above and indicated in FIG. 12 FIG. 16 shows an example of the oligonucleotides design for each subcassette.

Construction of the HIV Savine

Five of each group of ten designed oligonucleotides were spliced together using stepwise asymmetric PCR (Sandhu et al., 1992) and Splicing by Overlap Extension (SOEing) (FIG. 17 a). Each subcassette was then PCR amplified, cloned into pBluescript™ II KS⁻ using BamHI/EcoRI and 16 individual clones sequenced. Mutations, deletions and insertions were present in the large majority of the clones for each subcassette, despite acrylamide gel purification of the long oligonucleotides. In order to construct a fictional Savine with minimal mutations, two clones for each subcassette with no insertions or deletions and hence a complete open reading frame and with minimal numbers of non-designed mutations, were selected from the sixteen available. The subcassettes were then excised from their plasmids and joined by stepwise PCR-amplified ligation using the polymerase blend Elongase™ (Life Technology), T4 DNA ligase and the cohesive restriction enzymes XbaI/SpeI/AvrII/NheI, to generate two copies of cassettes A, B and C as outlined in FIG. 14 and shown in FIG. 17 b. Predicted sequences for these cassettes are shown in FIG. 30. Each cassette was then reamplifled by PCR with Elongase™, cloned into pBluescript™ II KS⁻ and 3 of the resulting plasmid clones sequenced using 12 of the 36 sequencing primers designed to cover the full length construct. Clones with minimal or no further mutations were selected for transfer into plasmids for DNA vaccination or used to make recombinant poxviruses. A summary of the number of designed and non-designed mutations in each Savine construct is presented in Table 1.

TABLE 1 Summary of mutations Number of mutations Expected Actual Construct No. aas Designed in 2 clones in 2 clones Non-designed Cassette A 1896 249 124 107  5 (AC1),  8 (AC2) Cassette B 1184 260 130 124 11 (BC1),  4 (BC2) Cassette C 1969 276 138 121 10 (CC1), 14 (CC2) Full length 5742 785 392 352 26 (FL1), 26 (FL2)

Summary of the mutations present in the two full-length clones constructed as determined by sequencing. Includes the number of mutations designed, expected and actually present in the 2 clones and the number of non-designed mutations in each cassette and full-length clone.

HIV Savine DNA vaccines and Recombinant Vaccinia viruses

To test the immunological effectiveness of the HIV Savine constructs the cassette sequences were transferred into DNA vaccine and poxvirus vectors. These vectors when used either separately in immunological assays described below or together in a ‘prime-boost ’ protocol which has been shown previously to generate strong T cell responses in vivo (Kent et al., 1997).

DNA Vaccination plasmids were constructed by excising the cassettes from the selected plasmid clones with XbaI/XhoI (cassette A) or XbaI/SalI (cassettes B and C) and ligating them into pDNAVacc cut with XbaI/XhoI to create pDVAC1, pDVAC2, pDVBC1, pDVBC2, pDVCC1, pDVCC2, respectively (FIG. 18 a). These plasmids were then further modified by cloning into their XbaI site a DNA fragment excised using XbaI/AvrII from pTUMERA2 and encoding a synthetic endoplasmic reticulum (ER) signal sequence from the Adenovirus E1A protein (Persson et al., 1980) (FIG. 18 a). ER signal sequences have been shown previously to enhance the presentation of both CTL and T helper epitopes in vivo (Ishioka, G.Y., 1999; Thomson et al., 1998). The plasmids pDVERAC1, pDVERBC1, pDVERCC1 andpDVERAC2, pDVERBC2, pDVERCC2 were then mixed together to create, plasmid pool 1 and pool 2 respectively. Each plasmid pool collectively encodes one copy of the designed full-length HIV Savine.

Plasmids to generate recombinant Vaccinia viruses which express HIV Savine sequences were constructed by excising the various HIV Savine cassettes from the selected plasmid clones using BamHI/XhoI (cassette A) or BamHI/SalI (cassettes B and C) and cloned into the marker rescue plasmid, pTK7.5, cleaved with BamHI/SalI. These pTK7.5-derived plasmids were then used to generate recombinant Vaccinia viruses by marker rescue recombination using established protocols (Boyle et al., 1985) to generate VV-AC1, VV-AC2, VV-BC1, VV-BC2, VV-CC1 and VV-CC2 (FIG. 18 b).

Two further DNA vaccine plasmids were constructed each encoding a version of the full length HIV Savine (FIG. 18 c). Briefly, the two versions of cassette B were excised with )XhoI and cloned into the corresponding selected plasmid clones containing cassette A sequences that were cut with XhoI/SalI to generate pBSAB 1 and pBSAB2 respectively. The joined A/B cassettes in pBSAB 1 and pBSAB2 were excised with XbaI/XhoI and cloned into pDVCC1 and pDVCC2, respectively, and cleaved with XbaI/XhoI to generate pDVFL1 and pDVFL2. These were then further modified to contain an ER signal sequence using the same cloning strategy as outlined in FIG. 18 a.

Restimulation of HIV specific lymphocytes from HIV infected patients

The present inventors examined the capacity of the HIV Savine to restimulate HIV-specific polyclonal CTL responses from HIV-infected patients. PBMCs from three different patients were restimulated in vitro with two HIV Savine Vaccinia virus pools (Pool 1 included VV-AC1 andVV-BC1; Pool 2 included VV-AC2, VV-BC2 and VV-CC2) then used in CTL lysis assays against LCLs infected either with one of the Savine Vaccinia virus pools or Vaccinia viruses which express gag, env or pol. FIG. 19 clearly shows, that in all three assays, both HIV Savine viral pools restimulated HIV-specific CTL responses which could recognise targets expressing whole natural HIV antigens and not targets which were uninfected or infected with the control Vaccinia virus. Furthermore, in all three cases, both pools restimulated responses that recognized all three natural HIV antigens. This result suggests that the combined Savine constructs will provide broader immunological coverage than single antigen based vaccine approaches. The level of lysis in each case of targets infected with Savine viral pools was significantly higher than the lysis recorded for any other infected target. This probably reflects the combined CTL responses to gag, pol, and env plus other HIV antigens not analyzed here but whose sequences are also incorporated into the Savine constructs.

CTL recognition of each HIV antigen is largely controlled by each patient's HLA background hence the pattern of CTL lysis for whole HIV antigens is different in each patient. Interestingly, this CTL lysis pattern did not change when the second Savine Vaccinia virus pool was used for CTL restimulation. In these assays, therefore, the inventors were unable to demonstrate clear differences between pools 1 and 2, despite pool 1 lacking a Vaccinia virus expressing cassette CC1 and despite the many amino acid differences between the A and B cassettes in each pool (see table 1).

From the foregoing, the present inventors have developed a novel vaccine/therapeutic strategy. In one embodiment, pathogen or cancer protein sequences are systemically fragmented, reverse translated back into DNA, rearranged randomly then joined back together. The designed synthetic DNA sequence is then constructed using long oligonucleotides and can be transferred into a range of delivery vectors. The vaccine vectors used here were DNA vaccine plasmids and recombinant poxvirus vectors which have been previously shown to elicit strong T cell responses when used together in a ‘prime-boost’ protocol (Kent et al., 1997). An important advantage of scrambled antigen vaccines or ‘Savines’ is that the amount of starting sequence information for the design can be easily expanded to include the majority of the protein sequences from a pathogen or for cancer, thereby providing the maximum possible vaccine or therapy coverage for a given population.

An embodiment of the systematic fragmentation approach described herein was based on the size and processing requirements for T cell epitopes and was designed to cause maximal disruption to the structure and function of protein sequences. This fragmentation approach ensures that the maximum possible range of T cell epitopes will be present from any incorporated protein sequence without the protein being functional and able to compromise vaccine safety

Another important advantage of Savines is that consensus protein sequences can be used for their design. This feature is only applicable when the design needs to cater for pathogen or cancer antigens whose sequence varies considerably. HIV is a highly mutagenic virus, hence this feature was utilized extensively to design a vaccine which has the potential to cover not only field isolates of HIV but also the major HIV clades involved in the current HIV pandemic. To construct the HIV Savine, one set of losynthesizedleotides was synthesized, which included degenerate bases in such a way that 8 constructs are theoretically required for the vaccine to contain all combinations in any stretch of 9 amino acids. The inventors believe that this approach can be improved for the following reasons: 1) While degenerate bases should be theoretically equally represented, in practice some degenerate bases were biased towards one base or the other, leading to a lower than expected frequency of the designed mutations in the two full length HIV Savines which were constructed (see Table 1). 2) Only sequence combinations actually present in the HIV lade consensus sequences are required to get full clade coverage, hence the number of full length constructs needed could be reduced. To reduce the number of constructs however, separate sets of long oligonucleotides would have to be synthesized, significantly increasing the cost, time and effort required to generate a vaccine capable of such considerable vaccine coverage.

A significant problem during the construction of the HIV Savine synthetic DNA sequence was the incorporation of non-designed mutations. The most serious types of mutations were insertions, deletions or those giving rise to stop codons, all of which change the frame of the synthesized sequences and/or caused premature truncation of the Savine proteins. These types of mutation were removed during construction of the HIV Savines by sequencing multiple clones after subcassette and cassette construction and selecting functional clones. The major source of these non-designed mutations was in the long oligonucleotides used for Savine synthesis, despite their gel purification. This problem could be reduced by making the initial subcassettes smaller thereby reducing the possibility of corrupted oligonucleotides being incorporated into each subcassette clone. The second major cause of non-designed mutations was the large number of PCR cycles required for the PCR and ligation-mediated joining of the subcassettes. Including extra sequencing and clone selection steps during the subcassette joining process should help to reduce the frequency of non-designed mutations in future constructs. Finally, another method that could help reduce the frequency of such mutations at all stages is to use resolvase treatment. Resolvases are bacteriophage-encoded endonucleases which recognise disruptions to double stranded DNA and are primarily used by bacteriophages to resolve Holliday junctions (Mizuuchi, 1982; Youil et al., 1995). T7 endonuclease I has already been used by the present inventors in synthetic DNA constructions to recognise mutations and cleave corrupted dsDNA to allow gel purification of correct sequences. Cleavage of corrupted sequences occurs because after a simple denaturing and hybridization step mutated DNA hybridizes to correct DNA sequences and results in a mispairing of DNA bases which is able to be recognized by the resolvase. This method resulted in a 50% reduction in the frequency of errors. Further optimization of this method and the use of a thermostable version of this type of enzyme could further reduce the frequency of errors during long Savine construction.

Two pools of Vaccinia viruses expressing Savine cassettes were both shown to restimulate HIV-specific responses from three different patients infected with B lade HIV viruses. These results provide a clear indication that the HIV Savine should provide broad coverage of the population because each patient had a different HLA pattern yet both pools were able to restimulate HIV-specific CTL responses in all three patients against all three natural HIV proteins tested. Also, both pools were shown to restimulate virtually identical CTL patterns in all three patients. This result was unexpected because some responses should have been lost or gained due to the amino acid differences between the two pools and because Pool 1 is only capable of expressing ⅔ of the full length HIV Savine. There are two suggested reasons why the pattern of CTL lysis was not altered between the two viral pools. Firstly, the sequences in the Savine constructs are nearly all duplicated because the fragment sequences overlap. Hence the loss of a third of the Savine may not have excluded sufficient T cell epitopes for differences to be detected in only three patient samples against only three HIV proteins. Secondly, while mutations often destroy T cell epitopes, if they remain functional, then the CTL they generate frequently can recognise alternate epitope sequences. Taken together this finding indirectly suggests that combining only two Savine constructs may provide robust multiclade coverage. Further experiments are being carried out to directly examine the capacity of the HIV Savine to stimulate CTL generated by different strains of HIV virus. The capacity of the two HIV-1 Savine Vaccinia vector pools to stimulate CD4+ T cell HIV-1 specific responses from infected patients was also tested (FIG. 20). Both patients showed significant proliferation of CD4+ T cells although both pools did not show consistent patterns suggesting that the two pools may provide wider vaccine coverage than using either pool independently.

The present inventors have generated a novel vaccine strategy, which has been used to generate what the inventors believe to be the most effective HIV candidate vaccine to date. The inventors have used this vaccine to immunize naive mice. FIG. 21 shows conclusively that the HIV-1 Savine described above can generate a Gag and Nef CTL response in naive mice. It should be noted, however, that the Nef CTL epitope appeared to exist only in Pool 1 since it was not restimulated by Pool 2. This is further proof of the utility of combining HIV-1 Savine Pool 1 and Pool 2 components together to provide broader vaccine coverage.

The HIV-1 Savine Vaccinia vectors have also been used to restimulate in vivo HIV-1 responses in pre-immune M. nemestrina monkeys. These experiments (FIG. 22) showed, by INF-γ ELISPOT and CD69 expression on both CD4 and CD8 T cells, that the ability of the HIV-1 SAVINE to restimulate HIV-1 specific responses in vivo is equivalent or perhaps better than another HIV-1 candidate vaccine.

This is a generic strategy able to be applied to many other human infections or cancers where T-cell responses are considered to be important for protection or recovery. With this in mind the inventors have begun constructing Savines for melanoma, cervical cancer and Hepatitis C. In the case of melanoma, the majority of the currently identified melanoma antigens have been divided into two groups, one containing antigens associated with melanoma and one containing differentiation antigens from melanocytes, which are often upregulated in melanomas. Two Savine constructs are presently being constructed to cater for these two groups. The reason for making the distinction is that treatment of melanoma might first proceed using the Savine that incorporates fragments of melanoma specific antigens only. If this Savine fails to control some metastases then the less specific Savine containing the melanocyte-specific antigens can then be used. It is important to point out that other cancers also express many of the antigens specific to melanomas e.g., testicular and breast cancers. Hence the melanoma specific Savine may have therapeutic benefits for other cancers.

A small Savine is also being constructed for cervical cancer. This Savine will contain two antigens, E6 and E7, from two strains of human papilloma virus (HPV), HPV-16 and HPV-18, directly linked with causing the majority of cervical cancers worldwide. There is a large number of sequence differences in these two antigens between the two strains which would normally require two Savines to be constructed. However since this Savine is small, the antigen fragments from both strains are being scrambled together. While it is normally better for the Savine approach to include all or a majority of the antigens from a virus, in this case only E6 and E7 are expressed during viral latency or in cervical carcinomas. Hence in the interests of simplicity, the rest of the HPV genome will not be included although all HPV antigens would be desirable in a Savine against genital warts.

Two Savines have also been constructed for two strains of hepatitis C, a major cause of liver disease in the world. Hepatitis C is similar to HIV in the requirements for a vaccine or therapeutic. However, the major hepatitis C strains share significantly lower homology, 69-79%, with one another than do the various HIV clades. To cater for this the inventors have decided to construct two separate constructs to cater for the two major strains present in Australia, types 1a and 3a, which together cause approximately 80-95% of hepatitis C infections in this country. Both constructs will be approximately the same size as the HIV Savine but will be blended together into a single vaccine or therapy.

Overall it is believed that the Savine vaccine strategy is a generic technology likely to be applied to a wide range of human diseases. It is also believed that because it is not necessary to characterize each antigen, this technology will be actively applied to animal vaccines as well where research into vaccines or therapies is often inhibited by the lack of specific reagents, modest research budgets and poor returns on animal vaccines.

Example 2 Hepatitis C Savine

Synthetic immunomodulatory molecules have also been designed for treating Hepatitis C. In one example, the algorithm of FIG. 25 was applied to a consensus polyprotein sequence of Hepatitis C1a to facilitate its segmentation into overlapping segments (30 aa segments overlapping by 15aa), the rearrangement of these segments into a scrambled order and the output of Savine nucleic acid and amino acid sequences, as shown in FIG. 26. Exemplary DNA cassettes (A, B and C) are also shown in FIG. 26, which contain suitable restriction enzyme sites at their ends to facilitate their joining into a single expressible open reading frame.

Example 3 Melanonia Savine

The algorithm of FIG. 25 was also applied to melanocyte differentiation antigens (gp100, MART, TRP-1, Tyros, Trp-2, MC1R, MUC1F and MUC1R) and to melanoma specific antigens (BAGE, GAGE-1, gp100In4, MAGE-1, MAGE-3, PRAME, TRP2IN2, NYNSO1a, NYNSO1b and LAGE1), as shown in FIG. 27, to provide separate Savine nucleic acid and amino acid sequences for treating or preventing melanoma.

Example 4 Resolvase Repair Experiment

A resolvase can be used advantageously to repair errors in polynucleotides. The following procedure outlines resolvase repair of a synthetic 340 bp fragment in which DNA errors were common.

Method

The 340 bp fragment was PCR amplified and gel purified on a 4% agarose gel. After spin purifying, 10 ul of the eluate corresponding to approximately 100 ng was subjected to the resolvase repair treatment. The rest of the DNA sample was stored for later cloning as the untreated control.

2 μL of 10×PCR buffer, 2 μL of 20 MM MgCl₂ and 6 μL of MilliQ™ water (MQW) and Taq DNA polymerase were added to the 10 μL DNA sample. The mixture was subjected to the following thermal profile; 95° C. for 5 min, 65° C. for 30 min, cooled and held at 37° C. Five μL of 10×T7 endonuclease I buffer, 8 μL of 1/50 μL of T7endoI enzyme stock and 17 μL of MQW were added, mixed and incubated for 30 min. Loading buffer was added to the sample and the sample was electrophoresed on a 4% agarose gel. A faint band corresponding to the full length fragment was excised and subjected to 15 further cycles of PCR. The amplified fragment was agarose gel purified and, along with the untreated DNA sample, cloned into pBluescript. Eleven plasmid clones for each DNA sample were sequenced and the number and type of errors compared (see table) Buffers were as follows:

10×T7Endonuclease Buffer

2.5 ml 1M TRIS pH7.8, 0.5 ml 1M MgCl₂, 25 μL 1 M DTT, 50 μL 10 mg/mL BSA, 2 mL MQW made up to a total of 5 mL.

T7 Endonuclease I Stock

Concentrated sample of enzyme prepared by, and obtained from, Jeff Babon (St Vincent's Hospital) was diluted 1/50 using the following dilution buffer: 50 μL 1 M TRIS pH7.8, 0.1 μL 1M EDTA pH8, 5 μL 100 mM glutathione, 50 μL 10 mg/mL BSA, 2.3 mL MQW, 2.5 mL glycerol made up to a total of 5 mL.

Results

The results are summarized in Tables 2 and 3.

TABLE 2 Total Errors Untreated Resolvase treated A/T to G/C = 6 A/T to G/C = 1 G/C to A/T = 12 G/C to A/T = 7 A/T to deletion = 1 A/T to deletion = 1 G/C to deletion = 6 G/C to deletion = 3

TABLE 3 Clone Summary Untreated Resolvase treated 6/11 contained deletions 3/11 contained deletions 9/11 contained mutations 7/11 contained mutations 2/11 correct 3/11 correct

DISCUSSION/CONCLUSION

While overall the number of correct clones obtained was not significantly different, there was a significant difference in the level of errors. This reduction in errors becomes more significant as greater numbers of long oligonucleotides are joined into the one construct i.e., increasing the difference between untreated versus treated samples in the chance of obtaining a correct clone. It is believed that combining another resolvase such as T4 endonuclease VII may further enhance repair or increase the bias against errors.

Importantly, this experiment was not optimized e.g., by using proofreading PCR enzymes or optimized conditions. Finally if the repair reaction is carried out during normal PCR, for example, by including a thermostable resolvase, it is believed that amplification of already damaged long oligonucleotides, and the normal accumulation of PCR induced errors, even using error reading polymerases during PCR, could be reduced significantly. The repair of damaged long oligonucleotides is particularly important for synthesis of long DNA fragment such as in Savines because, while the rate of long oligonucleotide damage is typically <5%, after joining 10 oligonucleotides, the error rate approaches 50%. This is true even using the best proofreading PCR enzymes because these enzymes do not verify the sequence integrity using correct oligonucleotide templates that exist as a significant majority (95%) in a joining reaction.

The disclosure of every patent, patent application, and publication cited herein is incorporated herein by reference in its entirety.

The citation of any reference herein should not be construed as an admission that such reference is available as “Prior Art” to the instant application

Throughout the specification the aim has been to describe the preferred embodiments of the invention without limiting the invention to any one embodiment or specific collection of features. Those of skill in the art will therefore appreciate that, in light of the instant disclosure, various modifications and changes can be made in the particular embodiments exemplified without departing from the scope of the present invention. All such modifications and changes are intended to be included within the scope of the appended claims.

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1. A synthetic polypeptide comprising at least three different segments of an HIV polypeptide, wherein the size of each segment is from about 20 to about 60 amino acids, wherein the segments are linked together in the same polypeptide chain but in a different relationship relative to their linkage in said HIV polypeptide, wherein the linkage of the segments impedes, abrogates or otherwise alters at least one function associated with said HIV polypeptide, wherein the sequence of any plurality of segments so linked is different from a sequence contained within said HIV polypeptide, wherein the sequence of at least one of said segments overlaps with the sequence of at least one other of said segments, wherein the sequence overlap is at least 4 contiguous amino acids in length, and wherein the synthetic polypeptide comprises at least 30% of the sequence of said HIV polypeptide.
 2. The synthetic polypeptide of claim 1, further comprising a segment from at least one other polypeptide.
 3. The synthetic polypeptide of claim 1, further comprising different segments from at least one other polypeptide, wherein the segments are linked together in a different relationship relative to their linkage in the at least one other polypeptide to impede, abrogate or otherwise alter at least one function associated with the at least one other polypeptide, and wherein the sequence of any plurality of segments so linked is different from a sequence contained within said at least one other polypeptide.
 4. The synthetic polypeptide of claim 1, wherein the segments in said synthetic polypeptide are linked sequentially in a different order or arrangement relative to their linkage in said HIV polypeptide.
 5. The synthetic polypeptide of claim 1, wherein the segments in said synthetic polypeptide are randomly rearranged relative to their linkage in said HIV polypeptide.
 6. The synthetic polypeptide of claim 1, wherein the size of an individual segment is from about 20 to about 30 amino acids.
 7. The synthetic polypeptide of claim 6, wherein the size of an individual segment is about 30 amino acids.
 8. The synthetic polypeptide of claim 1, wherein the sequence overlap is contained at one or both ends of an individual segment.
 9. The synthetic polypeptide of claim 1, wherein an optional spacer is interposed between some or all of the segments.
 10. The synthetic polypeptide of claim 9, wherein the spacer alters proteolytic processing and/or presentation of adjacent segment(s).
 11. The synthetic polypeptide of claim 10, wherein the spacer comprises at least one alanine residue.
 12. The synthetic polypeptide of claim 10, wherein the spacer comprises at least one alanine residue.
 13. The synthetic polypeptide of claim 1, wherein the at least one parent polypeptide is selected from the group consisting of env, gag, pol, vif, vpr, tat, rev, vpu and nef, or a combination thereof.
 14. A method for producing the synthetic polynucleotide according to claim 1, said method comprising: linking together in the same reading frame nucleic acid sequences encoding the plurality of different segments; and expressing the nucleotide sequences to produce said synthetic polypeptide.
 15. The method of claim 14, further comprising segmenting the sequence of an individual parent polypeptide into segments and linking said segments together in a different relationship relative to their linkage in the individual parent polypeptide sequence.
 16. The method of claim 15, wherein the segments are randomly linked together.
 17. The method of claim 14, further comprising reverse translating the sequence of an individual parent polypeptide or a segment thereof to provide a nucleic acid sequence encoding said parent polypeptide or said segment.
 18. The method of claim 17, wherein an amino acid of an individual parent polypeptide sequence is reverse translated to provide a codon, which has higher translational efficiency than other synonymous codons in a cell of interest.
 19. The method of claim 17, wherein an amino acid of an individual parent polypeptide sequence is reverse translated to provide a codon which, in the context of adjacent or local sequence elements, has a lower propensity of forming an undesirable sequence that is refractory to the execution of a task selected from the group consisting of cloning and sequencing.
 20. The method of claim 17, wherein an amino acid of an individual parent polypeptide sequence is reverse translated to provide a codon which, in the context of adjacent or local sequence elements, has a lower propensity of forming an undesirable sequence selected from a palindromic sequence or a duplicated sequence, which is refractory to the execution of a task selected from the group consisting of cloning or sequencing.
 21. The method of claim 14, further comprising linking a spacer oligonucleotide encoding at least one spacer residue between segment-encoding nucleic acids.
 22. The method of claim 21, wherein spacer oligonucleotide encodes 2 to 3 spacer residues.
 23. A composition comprising the synthetic polypeptide of claim 1, and a pharmaceutically acceptable carrier.
 24. The composition of claim 23, further comprising an adjuvant.
 25. A method for inducing an immune response comprising administering to a patient in need thereof an effective amount of an immunopotentiating agent selected from the group consisting of: a) the synthetic polypeptide of claim 1, b) a synthetic polynucleotide encoding the synthetic polypeptide of a) above, c) a synthetic construct comprising a synthetic polynucleotide encoding the synthetic polypeptide of b) above wherein the synthetic polynucleotide is operably linked to a regulatory polynucleotide, and d) a composition wherein said composition comprises an immunopotentiating agent selected from the group consisting of a) above, b) above and c) above, and a pharmaceutically acceptable carrier.
 26. The method of claim 24, wherein the spacer residue is a neutral amino acid.
 27. The method of claim 24, wherein the space residue is alanine.
 28. The method of claim 25, wherein the immune response is directed against HIV.
 29. The synthetic polypeptide of claim 1, wherein the overlap is about 15 amino acids.
 30. The synthetic polypeptide of claim 1, wherein said segments are from HIV gag or env.
 31. The synthetic peptide of claim 1, wherein said segments have a sequence selected from the group consisting of SEQ ID NOs: 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 281, 283, 285, 287, 289, 291, 293, 295, 297, and
 299. 32. The synthetic polypeptide of claim 1, wherein the sequence overlap is at least 7 contiguous amino acids in length.
 33. The synthetic polypeptide of claim 1, wherein the sequence overlap is at least 10 contiguous amino acids in length.
 34. The synthetic polypeptide of claim 1, wherein the sequence overlap is at least 15 contiguous amino acids in length.
 35. The synthetic polypeptide of claim 1, wherein the sequence overlap is at least 20 contiguous amino acids in length. 